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1. Newborn screening for Cerebrotendinous Xanthomatosis: A retrospective biomarker study using both flow-injection and UPLC-MS/MS analysis in newborns

Author

Vaz, Frederic M., Jamal, Youssra, Barto, Rob, Gelb, Michael H., DeBarber, Andrea E., Wevers, R.A., Nelen, M.R., Verrips, A., Salomons, Gajja S., and Huidekoper, H.H.

Subjects
All institutes and research themes of the Radboud University Medical Center, Other Research Radboud Institute for Health Sciences [Radboudumc 0], Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3]
Abstract

Contains fulltext : 288906.pdf (Publisher’s version ) (Open Access)

Published
2023

2. Optical genome mapping and revisiting short-read genome sequencing data reveal previously overlooked structural variants disrupting retinal disease-associated genes.

Author

Bruijn, S.E. de, Rodenburg, K., Corominas, J., Ben-Yosef, T., Reurink, J.A., Kremer, H., Whelan, L., Plomp, A.S., Berger, W., Farrar, G.J., Ferenc Kovács, Á., Fajardy, I., Hitti-Malin, R.J., Weisschuh, N., Weener, M.E., Sharon, D., Pennings, R.J.E., Haer-Wigman, L., Hoyng, C.B., Nelen, M.R., Vissers, L.E.L.M., Born, L.I. van den, Gilissen, C.F.H.A., Cremers, F.P.M., Hoischen, A., Neveling, K., Roosing, S., Bruijn, S.E. de, Rodenburg, K., Corominas, J., Ben-Yosef, T., Reurink, J.A., Kremer, H., Whelan, L., Plomp, A.S., Berger, W., Farrar, G.J., Ferenc Kovács, Á., Fajardy, I., Hitti-Malin, R.J., Weisschuh, N., Weener, M.E., Sharon, D., Pennings, R.J.E., Haer-Wigman, L., Hoyng, C.B., Nelen, M.R., Vissers, L.E.L.M., Born, L.I. van den, Gilissen, C.F.H.A., Cremers, F.P.M., Hoischen, A., Neveling, K., and Roosing, S.

Abstract

Item does not contain fulltext, PURPOSE: Structural variants (SVs) play an important role in inherited retinal diseases (IRD). Although the identification of SVs significantly improved upon the availability of genome sequencing, it is expected that involvement of SVs in IRDs is higher than anticipated. We revisited short-read genome sequencing data to enhance the identification of gene-disruptive SVs. METHODS: Optical genome mapping was performed to improve SV detection in short-read genome sequencing-negative cases. In addition, reanalysis of short-read genome sequencing data was performed to improve the interpretation of SVs and to re-establish SV prioritization criteria. RESULTS: In a monoallelic USH2A case, optical genome mapping identified a pericentric inversion (173 megabase), with 1 breakpoint disrupting USH2A. Retrospectively, the variant could be observed in genome sequencing data but was previously deemed false positive. Reanalysis of short-read genome sequencing data (427 IRD cases) was performed which yielded 30 pathogenic SVs affecting, among other genes, USH2A (n = 15), PRPF31 (n = 3), and EYS (n = 2). Eight of these (>25%) were overlooked during previous analyses. CONCLUSION: Critical evaluation of our findings allowed us to re-establish and improve our SV prioritization and interpretation guidelines, which will prevent missing pathogenic events in future analyses. Our data suggest that more attention should be paid to SV interpretation and the current contribution of SVs in IRDs is still underestimated.

Published
2023

3. The performance of genome sequencing as a first-tier test for neurodevelopmental disorders.

Author

Sanden, B. van der, Schobers, G.M.G., Corominas-Galbany, J., Koolen, D.A., Sinnema, M., Reeuwijk, J. van, Stumpel, C.T., Kleefstra, T., Vries, B.B. de, Ruiterkamp-Versteeg, M., Leijsten, N., Kwint, M.P., Derks, R.C., Swinkels, H.L., Ouden, A.P.M. den, Pfundt, R.P., Rinne, T.K., Leeuw, N. de, Stegmann, A.P.A., Stevens, S.J.C., Wijngaard, A. van den, Brunner, H.G., Yntema, H.G., Gilissen, C., Nelen, M.R., Vissers, L.E.L.M., Sanden, B. van der, Schobers, G.M.G., Corominas-Galbany, J., Koolen, D.A., Sinnema, M., Reeuwijk, J. van, Stumpel, C.T., Kleefstra, T., Vries, B.B. de, Ruiterkamp-Versteeg, M., Leijsten, N., Kwint, M.P., Derks, R.C., Swinkels, H.L., Ouden, A.P.M. den, Pfundt, R.P., Rinne, T.K., Leeuw, N. de, Stegmann, A.P.A., Stevens, S.J.C., Wijngaard, A. van den, Brunner, H.G., Yntema, H.G., Gilissen, C., Nelen, M.R., and Vissers, L.E.L.M.

Abstract

01 januari 2023, Item does not contain fulltext, Genome sequencing (GS) can identify novel diagnoses for patients who remain undiagnosed after routine diagnostic procedures. We tested whether GS is a better first-tier genetic diagnostic test than current standard of care (SOC) by assessing the technical and clinical validity of GS for patients with neurodevelopmental disorders (NDD). We performed both GS and exome sequencing in 150 consecutive NDD patient-parent trios. The primary outcome was diagnostic yield, calculated from disease-causing variants affecting exonic sequence of known NDD genes. GS (30%, n = 45) and SOC (28.7%, n = 43) had similar diagnostic yield. All 43 conclusive diagnoses obtained with SOC testing were also identified by GS. SOC, however, required integration of multiple test results to obtain these diagnoses. GS yielded two more conclusive diagnoses, and four more possible diagnoses than ES-based SOC (35 vs. 31). Interestingly, these six variants detected only by GS were copy number variants (CNVs). Our data demonstrate the technical and clinical validity of GS to serve as routine first-tier genetic test for patients with NDD. Although the additional diagnostic yield from GS is limited, GS comprehensively identified all variants in a single experiment, suggesting that GS constitutes a more efficient genetic diagnostic workflow.

Published
2023

4. Twist exome capture allows for lower average sequence coverage in clinical exome sequencing.

Author

Yaldiz, B., Kucuk, E., Hampstead, J.E., Hofste, Tom, Pfundt, R.P., Corominas-Galbany, J., Rinne, T.K., Yntema, H.G., Hoischen, A., Nelen, M.R., Gilissen, C.F.H.A., Yaldiz, B., Kucuk, E., Hampstead, J.E., Hofste, Tom, Pfundt, R.P., Corominas-Galbany, J., Rinne, T.K., Yntema, H.G., Hoischen, A., Nelen, M.R., and Gilissen, C.F.H.A.

Abstract

Item does not contain fulltext, BACKGROUND: Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. RESULTS: We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. CONCLUSION: We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.

Published
2023

5. Rapid exome sequencing as a first-tier test in neonates with suspected genetic disorder: results of a prospective multicenter clinical utility study in the Netherlands.

Author

Olde Keizer, R.A.C.M., Marouane, A., Kerstjens-Frederikse, W.S., Deden, A.C., Lichtenbelt, K.D., Jonckers, T., Vervoorn, M., Vreeburg, M., Henneman, L., Vries, L.S. de, Sinke, R.J., Pfundt, R.P., Stevens, S.J.C., Andriessen, P., Lingen, R.A. van, Nelen, M.R., Scheffer, H., Stemkens, D., Oosterwijk, C., Ploos van Amstel, H.K., Boode, W.P. de, Zelst-Stams, W.A.G. van, Frederix, G.W., Vissers, L.E.L.M., Olde Keizer, R.A.C.M., Marouane, A., Kerstjens-Frederikse, W.S., Deden, A.C., Lichtenbelt, K.D., Jonckers, T., Vervoorn, M., Vreeburg, M., Henneman, L., Vries, L.S. de, Sinke, R.J., Pfundt, R.P., Stevens, S.J.C., Andriessen, P., Lingen, R.A. van, Nelen, M.R., Scheffer, H., Stemkens, D., Oosterwijk, C., Ploos van Amstel, H.K., Boode, W.P. de, Zelst-Stams, W.A.G. van, Frederix, G.W., and Vissers, L.E.L.M.

Abstract

01 juni 2023, Contains fulltext : 293809.pdf (Publisher’s version ) (Open Access), The introduction of rapid exome sequencing (rES) for critically ill neonates admitted to the neonatal intensive care unit has made it possible to impact clinical decision-making. Unbiased prospective studies to quantify the impact of rES over routine genetic testing are, however, scarce. We performed a clinical utility study to compare rES to conventional genetic diagnostic workup for critically ill neonates with suspected genetic disorders. In a multicenter prospective parallel cohort study involving five Dutch NICUs, we performed rES in parallel to routine genetic testing for 60 neonates with a suspected genetic disorder and monitored diagnostic yield and the time to diagnosis. To assess the economic impact of rES, healthcare resource use was collected for all neonates. rES detected more conclusive genetic diagnoses than routine genetic testing (20% vs. 10%, respectively), in a significantly shorter time to diagnosis (15 days (95% CI 10-20) vs. 59 days (95% CI 23-98, p < 0.001)). Moreover, rES reduced genetic diagnostic costs by 1.5% (€85 per neonate). CONCLUSION: Our findings demonstrate the clinical utility of rES for critically ill neonates based on increased diagnostic yield, shorter time to diagnosis, and net healthcare savings. Our observations warrant the widespread implementation of rES as first-tier genetic test in critically ill neonates with disorders of suspected genetic origin. WHAT IS KNOWN: • Rapid exome sequencing (rES) enables diagnosing rare genetic disorders in a fast and reliable manner, but retrospective studies with neonates admitted to the neonatal intensive care unit (NICU) indicated that genetic disorders are likely underdiagnosed as rES is not routinely used. • Scenario modeling for implementation of rES for neonates with presumed genetic disorders indicated an expected increase in costs associated with genetic testing. WHAT IS NEW: • This unique prospective national clinical utility study of rES in a NICU setting shows that rES obtained

Published
2023

6. Towards Next-Generation Sequencing (NGS)-Based Newborn Screening: A Technical Study to Prepare for the Challenges Ahead

Author

Veldman, Abigail, Kiewiet, Mensiena B.G., Heiner-Fokkema, Margaretha Rebecca, Nelen, M.R., Sinke, R.J., Sikkema-Raddatz, Birgit, Westra, D., Schielen, Peter C.J.I., Spronsen, Francjan J. van, Veldman, Abigail, Kiewiet, Mensiena B.G., Heiner-Fokkema, Margaretha Rebecca, Nelen, M.R., Sinke, R.J., Sikkema-Raddatz, Birgit, Westra, D., Schielen, Peter C.J.I., and Spronsen, Francjan J. van

Abstract

Item does not contain fulltext

Published
2022

7. Reanalysis of exome negative patients with rare disease: a pragmatic workflow for diagnostic applications

Author

Schobers, G.M.G., Schieving, J.H., Yntema, H.G., Pennings, Maartje, Pfundt, R.P., Derks, R.C., Hofste, Tom, Wijs, I.J. de, Wieskamp, N.A., Heuvel, Simone van den, Corominas-Galbany, J., Gilissen, C.F.H.A., Nelen, M.R., Brunner, H.G., Kleefstra, T., Kamsteeg, E.J., Willemsen, M.A.A.P., Vissers, L.E.L.M., Schobers, G.M.G., Schieving, J.H., Yntema, H.G., Pennings, Maartje, Pfundt, R.P., Derks, R.C., Hofste, Tom, Wijs, I.J. de, Wieskamp, N.A., Heuvel, Simone van den, Corominas-Galbany, J., Gilissen, C.F.H.A., Nelen, M.R., Brunner, H.G., Kleefstra, T., Kamsteeg, E.J., Willemsen, M.A.A.P., and Vissers, L.E.L.M.

Abstract

Item does not contain fulltext

Published
2022

8. Megalobastic anemia, infantile leukemia, and immunodeficiency caused by a novel homozygous mutation in the DHFR gene

Author

Kuijpers, T.W., Vries, A.C.M. de, Leeuwen, E.M. van, Ermens, A., Pont, S., Smith, D.E., Wamelink, M.M., Mensenkamp, A.R., Nelen, M.R., Allen, H., Pals, S.T., Beverloo, B.H.B., Huidekoper, H.H., Wagner, A., Kuijpers, T.W., Vries, A.C.M. de, Leeuwen, E.M. van, Ermens, A., Pont, S., Smith, D.E., Wamelink, M.M., Mensenkamp, A.R., Nelen, M.R., Allen, H., Pals, S.T., Beverloo, B.H.B., Huidekoper, H.H., and Wagner, A.

Abstract

Item does not contain fulltext

Published
2022

9. Diagnostic analysis of the highly complex OPN1LW/OPN1MW gene cluster using long-read sequencing and MLPA

Author

Haer-Wigman, L., Ouden, A.P.M. den, Genderen, Maria m. van, Kroes, H.Y., Verheij, J., Smailhodzic, Dzenita, Blom, Jan, Derks, R.C., Yntema, H.G., Nelen, M.R., Vissers, L.E.L.M., Lugtenberg, D., Neveling, K., Haer-Wigman, L., Ouden, A.P.M. den, Genderen, Maria m. van, Kroes, H.Y., Verheij, J., Smailhodzic, Dzenita, Blom, Jan, Derks, R.C., Yntema, H.G., Nelen, M.R., Vissers, L.E.L.M., Lugtenberg, D., and Neveling, K.

Abstract

Contains fulltext : 285305.pdf (Publisher’s version ) (Open Access)

Published
2022

10. Clinical exome sequencing-Mistakes and caveats

Author

Corominas, J., Smeekens, S.P., Nelen, M.R., Yntema, H.G., Kamsteeg, E.J., Pfundt, R.P., Gilissen, C.F.H.A., Corominas, J., Smeekens, S.P., Nelen, M.R., Yntema, H.G., Kamsteeg, E.J., Pfundt, R.P., and Gilissen, C.F.H.A.

Abstract

Contains fulltext : 284807.pdf (Publisher’s version ) (Open Access), Massive parallel sequencing technology has become the predominant technique for genetic diagnostics and research. Many genetic laboratories have wrestled with the challenges of setting up genetic testing workflows based on a completely new technology. The learning curve we went through as a laboratory was accompanied by growing pains while we gained new knowledge and expertise. Here we discuss some important mistakes that have been made in our laboratory through 10 years of clinical exome sequencing but that have given us important new insights on how to adapt our working methods. We provide these examples and the lessons that we learned to help other laboratories avoid to make the same mistakes.

Published
2022

11. Long-read technologies identify a hidden inverted duplication in a family with choroideremia

Author

Fadaie, Z., Neveling, K., Mantere, T., Derks, R.C., Haer-Wigman, L., Ouden, A. Den, Kwint, M.P., O’Gorman, L., Valkenburg, D., Hoyng, C.B., Gilissen, C., Vissers, L.E.L.M., Nelen, M.R., Cremers, F.P.M., Hoischen, A., Roosing, S., Fadaie, Z., Neveling, K., Mantere, T., Derks, R.C., Haer-Wigman, L., Ouden, A. Den, Kwint, M.P., O’Gorman, L., Valkenburg, D., Hoyng, C.B., Gilissen, C., Vissers, L.E.L.M., Nelen, M.R., Cremers, F.P.M., Hoischen, A., and Roosing, S.

Abstract

Contains fulltext : 244033.pdf (Publisher’s version ) (Open Access)

Published
2021

12. Long-read trio sequencing of individuals with unsolved intellectual disability

Author

Pauper, M., Kucuk, E., Wenger, A.M., Chakraborty, S., Baybayan, P., Kwint, M., Sanden, B. van der, Nelen, M.R., Derks, R, Brunner, H.G., Hoischen, A., Vissers, L.E., Gilissen, C.F.H.A., Pauper, M., Kucuk, E., Wenger, A.M., Chakraborty, S., Baybayan, P., Kwint, M., Sanden, B. van der, Nelen, M.R., Derks, R, Brunner, H.G., Hoischen, A., Vissers, L.E., and Gilissen, C.F.H.A.

Abstract

Contains fulltext : 235027.pdf (Publisher’s version ) (Open Access), Long-read sequencing (LRS) has the potential to comprehensively identify all medically relevant genome variation, including variation commonly missed by short-read sequencing (SRS) approaches. To determine this potential, we performed LRS around 15×-40× genome coverage using the Pacific Biosciences Sequel I System for five trios. The respective probands were diagnosed with intellectual disability (ID) whose etiology remained unresolved after SRS exomes and genomes. Systematic assessment of LRS coverage showed that ~35 Mb of the human reference genome was only accessible by LRS and not SRS. Genome-wide structural variant (SV) calling yielded on average 28,292 SV calls per individual, totaling 12.9 Mb of sequence. Trio-based analyses which allowed to study segregation, showed concordance for up to 95% of these SV calls across the genome, and 80% of the LRS SV calls were not identified by SRS. De novo mutation analysis did not identify any de novo SVs, confirming that these are rare events. Because of high sequence coverage, we were also able to call single nucleotide substitutions. On average, we identified 3 million substitutions per genome, with a Mendelian inheritance concordance of up to 97%. Of these, ~100,000 were located in the ~35 Mb of the genome that was only captured by LRS. Moreover, these variants affected the coding sequence of 64 genes, including 32 known Mendelian disease genes. Our data show the potential added value of LRS compared to SRS for identifying medically relevant genome variation.

Published
2021

13. Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors

Author

Sabatella, M., Mantere, Tuomo, Waanders, E., Neveling, K., Mensenkamp, A.R., Dijk, F. van, Hehir, J.Y., Derks, R, Kwint, M.P., O'Gorman, L., Martins, M., Gidding, C.E.M., Lequin, M.H., Kusters, B., Wesseling, P., Nelen, M.R., Biegel, J.A., Hoischen, A., Jongmans, M.C.J., Kuiper, R.P., Sabatella, M., Mantere, Tuomo, Waanders, E., Neveling, K., Mensenkamp, A.R., Dijk, F. van, Hehir, J.Y., Derks, R, Kwint, M.P., O'Gorman, L., Martins, M., Gidding, C.E.M., Lequin, M.H., Kusters, B., Wesseling, P., Nelen, M.R., Biegel, J.A., Hoischen, A., Jongmans, M.C.J., and Kuiper, R.P.

Abstract

Item does not contain fulltext, In a subset of pediatric cancers, a germline cancer predisposition is highly suspected based on clinical and pathological findings, but genetic evidence is lacking, which hampers genetic counseling and predictive testing in the families involved. We describe a family with two siblings born from healthy parents who were both neonatally diagnosed with atypical teratoid rhabdoid tumor (ATRT). This rare and aggressive pediatric tumor is associated with biallelic inactivation of SMARCB1, and in 30% of the cases, a predisposing germline mutation is involved. Whereas the tumors of both siblings showed loss of expression of SMARCB1 and acquired homozygosity of the locus, whole exome and whole genome sequencing failed to identify germline or somatic SMARCB1 pathogenic mutations. We therefore hypothesized that the insertion of a pathogenic repeat-rich structure might hamper its detection, and we performed optical genome mapping (OGM) as an alternative strategy to identify structural variation in this locus. Using this approach, an insertion of ~2.8 kb within intron 2 of SMARCB1 was detected. Long-range PCR covering this region remained unsuccessful, but PacBio HiFi genome sequencing identified this insertion to be a SINE-VNTR-Alu, subfamily E (SVA-E) retrotransposon element, which was present in a mosaic state in the mother. This SVA-E insertion disrupts correct splicing of the gene, resulting in loss of a functional allele. This case demonstrates the power of OGM and long-read sequencing to identify genomic variations in high-risk cancer-predisposing genes that are refractory to detection with standard techniques, thereby completing the clinical and molecular diagnosis of such complex cases and greatly improving counseling and surveillance of the families involved. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Published
2021

14. Rapid whole exome sequencing in pregnancies to identify the underlying genetic cause in fetuses with congenital anomalies detected by ultrasound imaging

Author

Deden, A.C., Neveling, K., Zafeiropopoulou, D., Gilissen, C., Pfundt, R.P., Rinne, T.K., Leeuw, N. de, Faas, B.H., Gardeitchik, T., Sallevelt, S., Paulussen, A., Stevens, S.J.C., Sikkel, E., Elting, M.W., Maarle, M.C. van, Diderich, K.E.M., Corsten-Janssen, N., Lichtenbelt, K.D., Lachmeijer, G., Vissers, L.E.L.M., Yntema, H.G., Nelen, M.R., Feenstra, I., Zelst-Stams, W.A.G. van, Deden, A.C., Neveling, K., Zafeiropopoulou, D., Gilissen, C., Pfundt, R.P., Rinne, T.K., Leeuw, N. de, Faas, B.H., Gardeitchik, T., Sallevelt, S., Paulussen, A., Stevens, S.J.C., Sikkel, E., Elting, M.W., Maarle, M.C. van, Diderich, K.E.M., Corsten-Janssen, N., Lichtenbelt, K.D., Lachmeijer, G., Vissers, L.E.L.M., Yntema, H.G., Nelen, M.R., Feenstra, I., and Zelst-Stams, W.A.G. van

Abstract

Contains fulltext : 225140.pdf (Publisher’s version ) (Open Access), OBJECTIVE: The purpose of this study was to explore the diagnostic yield and clinical utility of trio-based rapid whole exome sequencing (rWES) in pregnancies of fetuses with a wide range of congenital anomalies detected by ultrasound imaging. METHODS: In this observational study, we analyzed the first 54 cases referred to our laboratory for prenatal rWES to support clinical decision making, after the sonographic detection of fetal congenital anomalies. The most common identified congenital anomalies were skeletal dysplasia (n = 20), multiple major fetal congenital anomalies (n = 17) and intracerebral structural anomalies (n = 7). RESULTS: A conclusive diagnosis was identified in 18 of the 54 cases (33%). Pathogenic variants were detected most often in fetuses with skeletal dysplasia (n = 11) followed by fetuses with multiple major fetal congenital anomalies (n = 4) and intracerebral structural anomalies (n = 3). A survey, completed by the physicians for 37 of 54 cases, indicated that the rWES results impacted clinical decision making in 68% of cases. CONCLUSIONS: These results suggest that rWES improves prenatal diagnosis of fetuses with congenital anomalies, and has an important impact on prenatal and peripartum parental and clinical decision making.

Published
2020

15. Presence of Genetic Variants Among Young Men With Severe COVID-19

Author

Made, C.I. van der, Simons, A., Schuurs-Hoeijmakers, J.H.M., Heuvel, Guus van den, Mantere, T., Kersten, S., Deuren, R.C. van, Steehouwer, M., Reijmersdal, S.V. van, Jaeger, M., Astuti, G.D., Corominas-Galbany, J., Hoeven, J.G. van der, Hagmolen of ten Have, W., Mast, Q. de, Bleeker-Rovers, C.P., Joosten, L.A.B., Yntema, H.G., Gilissen, C.F., Nelen, M.R., Meer, J.W.M. van der, Brunner, H.G., Netea, M.G., Veerdonk, F.L. van de, Hoischen, A., Made, C.I. van der, Simons, A., Schuurs-Hoeijmakers, J.H.M., Heuvel, Guus van den, Mantere, T., Kersten, S., Deuren, R.C. van, Steehouwer, M., Reijmersdal, S.V. van, Jaeger, M., Astuti, G.D., Corominas-Galbany, J., Hoeven, J.G. van der, Hagmolen of ten Have, W., Mast, Q. de, Bleeker-Rovers, C.P., Joosten, L.A.B., Yntema, H.G., Gilissen, C.F., Nelen, M.R., Meer, J.W.M. van der, Brunner, H.G., Netea, M.G., Veerdonk, F.L. van de, and Hoischen, A.

Abstract

Contains fulltext : 222168.pdf (Publisher’s version ) (Closed access)

Published
2020

16. Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

Author

Arts, P., Simons, A., AlZahrani, Mofareh S., Yilmaz, Elanur, AlIdrissi, Eman, Aerde, K.J. van, Bleeker-Rovers, C.P., Deuren, M. van, Flier, M. van der, Gilissen, C., Hehir-Kwa, J.Y., Henriet, S.S., Hoppenreijs, E.P., MacKenzie, M.A., Mensenkamp, A.R., Nelen, M.R., Oever, J. ten, Schuurs-Hoeijmakers, J.H.M., Simon, A., Vorst, M. van de, Veltman, J.A., Zelst-Stams, W.A.G. van, Veerdonk, F.L. van de, Netea, M.G., Hoischen, A., Arts, P., Simons, A., AlZahrani, Mofareh S., Yilmaz, Elanur, AlIdrissi, Eman, Aerde, K.J. van, Bleeker-Rovers, C.P., Deuren, M. van, Flier, M. van der, Gilissen, C., Hehir-Kwa, J.Y., Henriet, S.S., Hoppenreijs, E.P., MacKenzie, M.A., Mensenkamp, A.R., Nelen, M.R., Oever, J. ten, Schuurs-Hoeijmakers, J.H.M., Simon, A., Vorst, M. van de, Veltman, J.A., Zelst-Stams, W.A.G. van, Veerdonk, F.L. van de, Netea, M.G., and Hoischen, A.

Abstract

Contains fulltext : 204759.pdf (publisher's version ) (Open Access)

Published
2019

17. BRCA Testing by Single-Molecule Molecular Inversion Probes

Author

Neveling, K., Mensenkamp, A.R., Derks, R, Kwint, M.P., Ouchene, H., Steehouwer, M., Lier, L.A. van, Bosgoed, E.A.J., Rikken, A., Tychon, M.W.J., Zafeiropoulou, D., Castelein, S., Hehir-Kwa, J.Y., Thung, G.W., Hofste, T., Lelieveld, S.H., Bertens, S.M., Adan, I.B., Eijkelenboom, A., Tops, B.B.J., Yntema, H.G., Stokowy, T., Knappskog, P.M., Hoberg-Vetti, H., Steen, V.M., Boyle, E., Martin, B., Ligtenberg, M.J.L., Shendure, J., Nelen, M.R., Hoischen, A., Neveling, K., Mensenkamp, A.R., Derks, R, Kwint, M.P., Ouchene, H., Steehouwer, M., Lier, L.A. van, Bosgoed, E.A.J., Rikken, A., Tychon, M.W.J., Zafeiropoulou, D., Castelein, S., Hehir-Kwa, J.Y., Thung, G.W., Hofste, T., Lelieveld, S.H., Bertens, S.M., Adan, I.B., Eijkelenboom, A., Tops, B.B.J., Yntema, H.G., Stokowy, T., Knappskog, P.M., Hoberg-Vetti, H., Steen, V.M., Boyle, E., Martin, B., Ligtenberg, M.J.L., Shendure, J., Nelen, M.R., and Hoischen, A.

Abstract

Contains fulltext : 169902.pdf (publisher's version ) (Closed access), BACKGROUND: Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS: The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS: Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10-15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS: smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.

Published
2017

18. Novel BRCA1 and BRCA2 Tumor Test as Basis for Treatment Decisions and Referral for Genetic Counselling of Patients with Ovarian Carcinomas.

Author

Weren, R.D.A., Mensenkamp, A.R., Simons, M., Eijkelenboom, A., Sie, A.S., Ouchene, H., Asseldonk, M. van, Gomez-Garcia, E.B., Blok, M.J., Hullu, J.A. de, Nelen, M.R., Hoischen, A., Bulten, J., Tops, B.B.J., Hoogerbrugge, N., Ligtenberg, M.J.L., Weren, R.D.A., Mensenkamp, A.R., Simons, M., Eijkelenboom, A., Sie, A.S., Ouchene, H., Asseldonk, M. van, Gomez-Garcia, E.B., Blok, M.J., Hullu, J.A. de, Nelen, M.R., Hoischen, A., Bulten, J., Tops, B.B.J., Hoogerbrugge, N., and Ligtenberg, M.J.L.

Abstract

Contains fulltext : 170272.pdf (publisher's version ) (Open Access)

Published
2017

19. Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders

Author

Pfundt, R.P., Rosario, M. del, Vissers, L.E.L.M., Kwint, M.P., Janssen, I.M., Leeuw, N. de, Yntema, H.G., Nelen, M.R., Lugtenberg, D., Kamsteeg, E.J., Wieskamp, N.A., Stegmann, A.P., Stevens, S.J., Rodenburg, R.J.T., Simons, A., Mensenkamp, A.R., Rinne, T.K., Gilissen, C.F., Scheffer, H., Veltman, J.A., Hehir-Kwa, J.Y., Pfundt, R.P., Rosario, M. del, Vissers, L.E.L.M., Kwint, M.P., Janssen, I.M., Leeuw, N. de, Yntema, H.G., Nelen, M.R., Lugtenberg, D., Kamsteeg, E.J., Wieskamp, N.A., Stegmann, A.P., Stevens, S.J., Rodenburg, R.J.T., Simons, A., Mensenkamp, A.R., Rinne, T.K., Gilissen, C.F., Scheffer, H., Veltman, J.A., and Hehir-Kwa, J.Y.

Abstract

Contains fulltext : 174063.pdf (publisher's version ) (Open Access), PURPOSE: Copy-number variation is a common source of genomic variation and an important genetic cause of disease. Microarray-based analysis of copy-number variants (CNVs) has become a first-tier diagnostic test for patients with neurodevelopmental disorders, with a diagnostic yield of 10-20%. However, for most other genetic disorders, the role of CNVs is less clear and most diagnostic genetic studies are generally limited to the study of single-nucleotide variants (SNVs) and other small variants. With the introduction of exome and genome sequencing, it is now possible to detect both SNVs and CNVs using an exome- or genome-wide approach with a single test. METHODS: We performed exome-based read-depth CNV screening on data from 2,603 patients affected by a range of genetic disorders for which exome sequencing was performed in a diagnostic setting. RESULTS: In total, 123 clinically relevant CNVs ranging in size from 727 bp to 15.3 Mb were detected, which resulted in 51 conclusive diagnoses and an overall increase in diagnostic yield of ~2% (ranging from 0 to -5.8% per disorder). CONCLUSIONS: This study shows that CNVs play an important role in a broad range of genetic disorders and that detection via exome-based CNV profiling results in an increase in the diagnostic yield without additional testing, bringing us closer to single-test genomics.Genet Med advance online publication 27 October 2016.

Published
2017

20. Diagnostic exome sequencing in 266 Dutch patients with visual impairment

Author

Haer-Wigman, L., Zelst-Stams, W.A.G. van, Pfundt, R.P., Born, L.I. van den, Klaver, C.C.W., Verheij, J.B.G.M., Hoyng, C.B., Breuning, M.H., Boon, C.J.F., Kievit, A.J., Verhoeven, V.J., Pott, J.W., Sallevelt, S.C., Hagen, J.M. van, Plomp, A.S., Kroes, H.Y., Lelieveld, S.H., Hehir-Kwa, J.Y., Castelein, S., Nelen, M.R., Scheffer, H., Lugtenberg, D., Cremers, F.P.M., Hoefsloot, L., Yntema, H.G., Haer-Wigman, L., Zelst-Stams, W.A.G. van, Pfundt, R.P., Born, L.I. van den, Klaver, C.C.W., Verheij, J.B.G.M., Hoyng, C.B., Breuning, M.H., Boon, C.J.F., Kievit, A.J., Verhoeven, V.J., Pott, J.W., Sallevelt, S.C., Hagen, J.M. van, Plomp, A.S., Kroes, H.Y., Lelieveld, S.H., Hehir-Kwa, J.Y., Castelein, S., Nelen, M.R., Scheffer, H., Lugtenberg, D., Cremers, F.P.M., Hoefsloot, L., and Yntema, H.G.

Abstract

Contains fulltext : 174726.pdf (publisher's version ) (Open Access), Inherited eye disorders have a large clinical and genetic heterogeneity, which makes genetic diagnosis cumbersome. An exome-sequencing approach was developed in which data analysis was divided into two steps: the vision gene panel and exome analysis. In the vision gene panel analysis, variants in genes known to cause inherited eye disorders were assessed for pathogenicity. If no causative variants were detected and when the patient consented, the entire exome data was analyzed. A total of 266 Dutch patients with different types of inherited eye disorders, including inherited retinal dystrophies, cataract, developmental eye disorders and optic atrophy, were investigated. In the vision gene panel analysis (likely), causative variants were detected in 49% and in the exome analysis in an additional 2% of the patients. The highest detection rate of (likely) causative variants was in patients with inherited retinal dystrophies, for instance a yield of 63% in patients with retinitis pigmentosa. In patients with developmental eye defects, cataract and optic atrophy, the detection rate was 50, 33 and 17%, respectively. An exome-sequencing approach enables a genetic diagnosis in patients with different types of inherited eye disorders using one test. The exome approach has the same detection rate as targeted panel sequencing tests, but offers a number of advantages. For instance, the vision gene panel can be frequently and easily updated with additional (novel) eye disorder genes. Determination of the genetic diagnosis improved the clinical diagnosis, regarding the assessment of the inheritance pattern as well as future disease perspective.

Published
2017

21. The diagnostic yield of whole-exome sequencing targeting a gene panel for hearing impairment in The Netherlands

Author

Zazo Seco, C., Wesdorp, F.M., Feenstra, I., Pfundt, R.P., Hehir-Kwa, J.Y., Lelieveld, S.H., Castelein, S., Gilissen, C.F., Wijs, I.J. de, Admiraal, R.J.C., Pennings, R.J.E., Kunst, H.P.M., Kamp, J.M. van de, Tamminga, S., Houweling, A.C., Plomp, A.S., Maas, S.M., Koning-Gans, P.A. de, Kant, S.G., Geus, C.M. de, Frints, S.G., Vanhoutte, E.K., Dooren, M.F. van, Boogaard, M.J. van den, Scheffer, H., Nelen, M.R., Kremer, H., Hoefsloot, L.H., Schraders, M., Yntema, H.G., Zazo Seco, C., Wesdorp, F.M., Feenstra, I., Pfundt, R.P., Hehir-Kwa, J.Y., Lelieveld, S.H., Castelein, S., Gilissen, C.F., Wijs, I.J. de, Admiraal, R.J.C., Pennings, R.J.E., Kunst, H.P.M., Kamp, J.M. van de, Tamminga, S., Houweling, A.C., Plomp, A.S., Maas, S.M., Koning-Gans, P.A. de, Kant, S.G., Geus, C.M. de, Frints, S.G., Vanhoutte, E.K., Dooren, M.F. van, Boogaard, M.J. van den, Scheffer, H., Nelen, M.R., Kremer, H., Hoefsloot, L.H., Schraders, M., and Yntema, H.G.

Abstract

Contains fulltext : 169850.pdf (publisher's version ) (Closed access), Hearing impairment (HI) is genetically heterogeneous which hampers genetic counseling and molecular diagnosis. Testing of several single HI-related genes is laborious and expensive. In this study, we evaluate the diagnostic utility of whole-exome sequencing (WES) targeting a panel of HI-related genes. Two hundred index patients, mostly of Dutch origin, with presumed hereditary HI underwent WES followed by targeted analysis of an HI gene panel of 120 genes. We found causative variants underlying the HI in 67 of 200 patients (33.5%). Eight of these patients have a large homozygous deletion involving STRC, OTOA or USH2A, which could only be identified by copy number variation detection. Variants of uncertain significance were found in 10 patients (5.0%). In the remaining 123 cases, no potentially causative variants were detected (61.5%). In our patient cohort, causative variants in GJB2, USH2A, MYO15A and STRC, and in MYO6 were the leading causes for autosomal recessive and dominant HI, respectively. Segregation analysis and functional analyses of variants of uncertain significance will probably further increase the diagnostic yield of WES.

Published
2017

22. The diagnostic yield of whole-exome sequencing targeting a gene panel for hearing impairment in the Netherlands

Author

Seco, C.Z. (Celia Zazo), Wesdorp, M. (Mieke), Feenstra, I. (Ilse), Pfundt, R. (Rolph), Hehir-Kwa, J. (Jayne), Lelieveld, S.H. (Stefan H.), Castelein, S. (Steven), Gilissen, C. (Christian), Wijs, I.J. (Ilse) de, Admiraal, R.J. (Ronald), Pennings, R.J.E. (Ronald J.E.), Kunst, H.P.M. (Henricus P.M.), van de Kamp, J.M. (Jiddeke M.), Tamminga, S. (Saskia), Houweling, A.C. (Arjan), Plomp, A. (Astrid), Maas, S.M. (Saskia), de Koning Gans, P.A.M. (P. A M), Kant, S.G. (Sarina), De Geus, C.M. (Christa M.), Frints, S.G.M. (Suzanna), Vanhoutte, E.K. (Els), Dooren, M.F. (Marieke) van, Boogaard, M.H. (Marie-José Henriëtte) van den, Scheffer, H. (Hans), Nelen, M.R. (Marcel), Kremer, H. (Hannie), Hoefsloot, E.H. (Lies), Schraders, M. (Margit), Yntema, H.G., Seco, C.Z. (Celia Zazo), Wesdorp, M. (Mieke), Feenstra, I. (Ilse), Pfundt, R. (Rolph), Hehir-Kwa, J. (Jayne), Lelieveld, S.H. (Stefan H.), Castelein, S. (Steven), Gilissen, C. (Christian), Wijs, I.J. (Ilse) de, Admiraal, R.J. (Ronald), Pennings, R.J.E. (Ronald J.E.), Kunst, H.P.M. (Henricus P.M.), van de Kamp, J.M. (Jiddeke M.), Tamminga, S. (Saskia), Houweling, A.C. (Arjan), Plomp, A. (Astrid), Maas, S.M. (Saskia), de Koning Gans, P.A.M. (P. A M), Kant, S.G. (Sarina), De Geus, C.M. (Christa M.), Frints, S.G.M. (Suzanna), Vanhoutte, E.K. (Els), Dooren, M.F. (Marieke) van, Boogaard, M.H. (Marie-José Henriëtte) van den, Scheffer, H. (Hans), Nelen, M.R. (Marcel), Kremer, H. (Hannie), Hoefsloot, E.H. (Lies), Schraders, M. (Margit), and Yntema, H.G.

Abstract

Hearing impairment (HI) is genetically heterogeneous which hampers genetic counseling and molecular diagnosis. Testing of several single HI-related genes is laborious and expensive. In this study, we evaluate the diagnostic utility of whole-exome sequencing (WES) targeting a panel of HI-related genes. Two hundred index patients, mostly of Dutch origin, with presumed hereditary HI underwent WES followed by targeted analysis of an HI gene panel of 120 genes. We found causative variants underlying the HI in 67 of 200 patients (33.5%). Eight of these patients have a large homozygous deletion involving STRC, OTOA or USH2A, which could only be identified by copy number variation detection. Variants of uncertain significance were found in 10 patients (5.0%). In the remaining 123 cases, no potentially causative variants were detected (61.5%). In our patient cohort, causative variants in GJB2, USH2A, MYO15A and STRC, and in MYO6 were the leading causes for autosomal recessive and dominant HI, respectively. Segregation analysis and functional analyses of variants of uncertain significance will probably further increase the diagnostic yield of WES.

Published
2017
Full Text
View/download PDF

23. Diagnostic exome sequencing in 266 Dutch patients with visual impairment

Author

Haer-Wigman, L. (Lonneke), Zelst-Stams, W.A. van, Pfundt, R. (Rolph), Born, L.I. (Ingeborgh) van den, Klaver, C.C.W. (Caroline), Verheij, J.B. (Joke), Hoyng, C.B. (Carel), Breuning, M.H. (Martijn), Boon, C.J.F. (Camiel), Kievit, A.J.A. (Anneke J.A.), Verhoeven, V.J.M. (Virginie), Pott, J.W.R., Sallevelt, S.C.E.H. (Suzanne), Hagen, J.M. (Johanna) van, Plomp, A. (Astrid), Kroes, H.Y. (Hester), Lelieveld, S.H. (Stefan H.), Hehir-Kwa, J. (Jayne), Castelein, S. (Steven), Nelen, M.R. (Marcel), Scheffer, H. (Hans), Lugtenberg, D. (Dorien), Cremers, F.P.M. (Frans), Hoefsloot, E.H. (Lies), Yntema, H.G., Haer-Wigman, L. (Lonneke), Zelst-Stams, W.A. van, Pfundt, R. (Rolph), Born, L.I. (Ingeborgh) van den, Klaver, C.C.W. (Caroline), Verheij, J.B. (Joke), Hoyng, C.B. (Carel), Breuning, M.H. (Martijn), Boon, C.J.F. (Camiel), Kievit, A.J.A. (Anneke J.A.), Verhoeven, V.J.M. (Virginie), Pott, J.W.R., Sallevelt, S.C.E.H. (Suzanne), Hagen, J.M. (Johanna) van, Plomp, A. (Astrid), Kroes, H.Y. (Hester), Lelieveld, S.H. (Stefan H.), Hehir-Kwa, J. (Jayne), Castelein, S. (Steven), Nelen, M.R. (Marcel), Scheffer, H. (Hans), Lugtenberg, D. (Dorien), Cremers, F.P.M. (Frans), Hoefsloot, E.H. (Lies), and Yntema, H.G.

Abstract

Inherited eye disorders have a large clinical and genetic heterogeneity, which makes genetic diagnosis cumbersome. An exome-sequencing approach was developed in which data analysis was divided into two steps: the vision gene panel and exome analysis. In the vision gene panel analysis, variants in genes known to cause inherited eye disorders were assessed for pathogenicity. If no causative variants were detected and when the patient consented, the entire exome data was analyzed. A total of 266 Dutch patients with different types of inherited eye disorders, including inherited retinal dystrophies, cataract, developmental eye disorders and optic atrophy, were investigated. In the vision gene panel analysis (likely), causative variants were detected in 49% and in the exome analysis in an additional 2% of the patients. The highest detection rate of (likely) causative variants was in patients with inherited retinal dystrophies, for instance a yield of 63% in patients with retinitis pigmentosa. In patients with developmental eye defects, cataract and optic atrophy, the detection rate was 50, 33 and 17%, respectively. An exome-sequencing approach enables a genetic diagnosis in patients with different types of inherited eye disorders using one test. The exome approach has the same detection rate as targeted panel sequencing tests, but offers a number of advantages. For instance, the vision gene panel can be frequently and easily updated with additional (novel) eye disorder genes. Determination of the genetic diagnosis improved the clinical diagnosis, regarding the assessment of the inheritance pattern as well as future disease perspective.

Published
2017
Full Text
View/download PDF

24. A molecular inversion probe-based next-generation sequencing panel to detect germline mutations in Chinese early-onset colorectal cancer patients.

Author

Zhang, J., Wang, W., Voer, R.M. de, Hehir-Kwa, J.Y., Kamping, E.J., Weren, R.D.A., Nelen, M.R., Hoischen, A., Ligtenberg, M.J.L., Hoogerbrugge, N., Yang, X, Yang, Z, Fan, X., Wang, L., Liu, H., Wang, J, Kuiper, R.P., Geurts van Kessel, A.H.M., Zhang, J., Wang, W., Voer, R.M. de, Hehir-Kwa, J.Y., Kamping, E.J., Weren, R.D.A., Nelen, M.R., Hoischen, A., Ligtenberg, M.J.L., Hoogerbrugge, N., Yang, X, Yang, Z, Fan, X., Wang, L., Liu, H., Wang, J, Kuiper, R.P., and Geurts van Kessel, A.H.M.

Abstract

Contains fulltext : 169654.pdf (publisher's version ) (Open Access)

Published
2017

25. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability

Author

Lelieveld, S.H., Reijnders, M.R.F., Pfundt, R.P., Yntema, H.G., Kamsteeg, E.J., Vries, P.F. de, Vries, B.B. de, Willemsen, M.H., Kleefstra, T., Lohner, K., Vreeburg, M., Stevens, S.J., Burgt, I. van der, Bongers, E.M., Stegmann, A.P., Rump, P., Rinne, T.K., Nelen, M.R., Veltman, J.A., Vissers, L.E., Brunner, H.G., Gilissen, C.F., Lelieveld, S.H., Reijnders, M.R.F., Pfundt, R.P., Yntema, H.G., Kamsteeg, E.J., Vries, P.F. de, Vries, B.B. de, Willemsen, M.H., Kleefstra, T., Lohner, K., Vreeburg, M., Stevens, S.J., Burgt, I. van der, Bongers, E.M., Stegmann, A.P., Rump, P., Rinne, T.K., Nelen, M.R., Veltman, J.A., Vissers, L.E., Brunner, H.G., and Gilissen, C.F.

Abstract

Item does not contain fulltext, To identify candidate genes for intellectual disability, we performed a meta-analysis on 2,637 de novo mutations, identified from the exomes of 2,104 patient-parent trios. Statistical analyses identified 10 new candidate ID genes: DLG4, PPM1D, RAC1, SMAD6, SON, SOX5, SYNCRIP, TCF20, TLK2 and TRIP12. In addition, we show that these genes are intolerant to nonsynonymous variation and that mutations in these genes are associated with specific clinical ID phenotypes.

Published
2016

26. Is the $1000 Genome as Near as We Think? A Cost Analysis of Next-Generation Sequencing

Author

Nimwegen, K.J.M. van, Soest, R.A., Veltman, J.A., Nelen, M.R., Wilt, G.J. van der, Peart-Vissers, L.E.L.M., Grutters, J.P.C., Nimwegen, K.J.M. van, Soest, R.A., Veltman, J.A., Nelen, M.R., Wilt, G.J. van der, Peart-Vissers, L.E.L.M., and Grutters, J.P.C.

Abstract

Contains fulltext : 167905.pdf (publisher's version ) (Closed access), BACKGROUND: The substantial technological advancements in next-generation sequencing (NGS), combined with dropping costs, have allowed for a swift diffusion of NGS applications in clinical settings. Although several commercial parties report to have broken the $1000 barrier for sequencing an entire human genome, a valid cost overview for NGS is currently lacking. This study provides a complete, transparent and up-to-date overview of the total costs of different NGS applications. METHODS: Cost calculations for targeted gene panels (TGP), whole exome sequencing (WES) and whole genome sequencing (WGS) were based on the Illumina NextSeq500, HiSeq4000, and HiSeqX5 platforms, respectively. To anticipate future developments, sensitivity analyses are performed. RESULTS: Per-sample costs were euro1669 for WGS, euro 792 for WES and euro333 for TGP. To reach the coveted $1000 genome, not only is the long-term and efficient use of the sequencing equipment needed, but also large reductions in capital costs and especially consumable costs are also required. CONCLUSIONS: WES and TGP are considerably lower-cost alternatives to WGS. However, this does not imply that these NGS approaches should be preferred in clinical practice, since this should be based on the tradeoff between costs and the expected clinical utility of the approach chosen. The results of the present study contribute to the evaluation of such tradeoffs.

Published
2016

27. Reliable Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue Using Single Molecule Tags

Author

Eijkelenboom, A., Kamping, E.J., Raaij, A.W. van, Hendriks-Cornelissen, S.J., Neveling, K., Kuiper, R.P., Hoischen, A., Nelen, M.R., Ligtenberg, M.J.L., Tops, B.B.J., Eijkelenboom, A., Kamping, E.J., Raaij, A.W. van, Hendriks-Cornelissen, S.J., Neveling, K., Kuiper, R.P., Hoischen, A., Nelen, M.R., Ligtenberg, M.J.L., and Tops, B.B.J.

Abstract

Contains fulltext : 168105.pdf (publisher's version ) (Open Access), Sequencing of tumor DNA to detect genetic aberrations is becoming increasingly important, not only to refine cancer diagnoses but also to predict response to targeted treatments. Next-generation sequencing is widely adopted in diagnostics for the analyses of DNA extracted from routinely processed formalin-fixed, paraffin-embedded tissue, fine-needle aspirates, or cytologic smears. PCR-based enrichment strategies are usually required to obtain sufficient read depth for reliable detection of genetic aberrations. However, although the read depth relates to sensitivity and specificity, PCR duplicates generated during target enrichment may result in overestimation of library complexity, which may result in false-negative results. Here, we report the validation of a 23-gene panel covering 41 hotspot regions using single-molecule tagging of DNA molecules by single-molecule molecular inversion probes (smMIPs), allowing assessment of library complexity. The smMIP approach outperforms Sanger and Ampliseq-Personal Genome Machine-based sequencing in our clinical diagnostic setting. Furthermore, single-molecule tags allow consensus sequence read formation, allowing detection to 1% allele frequency and reliable exclusion of variants to 3%. The number of false-positive calls is also markedly reduced (>10-fold), and our panel design allows for distinction between true mutations and deamination artifacts. Not only is this technique superior, smMIP-based library preparation is also scalable, easy to automate, and flexible. We have thus implemented this approach for sequence analysis of clinical samples in our routine diagnostic workflow.

Published
2016

28. PTEN mutation analysis in two genetic subtypes of high-grade oligodendroglial tumors: PTEN is only occasionally mutated in one of the two genetic subtypes

Author

Jeuken, J.W.M., Nelen, M.R., Vermeer, H., Staveren, W.A. van, Kremer, J.M.J., Overbeeke, J.J. van, and Boerman, R.H.

Subjects
Genetische analyse van oligodendrogliomas en oligoastrocytomas, Genetic analysis of oligodendrogiomas and mixed tumors, Positional cloning of the gene for Cowden disease and investigating the importance of mutations in this gene for the development of various tumors, Positionele clonering van het gen voor de ziekte van Cowden en onderzoek naar de rol van mutaties in dit gen bij een aantal typen tumoren
Abstract

Item does not contain fulltext

Published
2000

29. Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects

Author

Vrijenhoek, T., Kraaijeveld, K., Elferink, M., Ligt, J. de, Kranendonk, E., Santen, G., Nijman, IJ, Butler, D., Claes, G., Costessi, A., Dorlijn, W., Eyndhoven, W. van, Halley, D.J., Hout, M.C. van den, Hove, S. van, Johansson, L.F., Jongbloed, J.D., Kamps, R., Kockx, C.E., Koning, B. de, Kriek, M., Deprez, R.L., Lunstroo, H., Mannens, M., Mook, O.R., Nelen, M.R., Ploem, C., Rijnen, M., Saris, J.J., Sinke, R., Sistermans, E., Slegtenhorst, M. van, Sleutels, F., Stoep, N. van der, Tienhoven, M. van, Vermaat, M., Vogel, M., Waisfisz, Q., Weiss, J.M., Wijngaard, A. van den, Workum, W. van, IJntema, H., Zwaag, B. van der, van, I.W.F., Dunnen, J.T. den, Veltman, J.A., Hennekam, R., Cuppen, E., Vrijenhoek, T., Kraaijeveld, K., Elferink, M., Ligt, J. de, Kranendonk, E., Santen, G., Nijman, IJ, Butler, D., Claes, G., Costessi, A., Dorlijn, W., Eyndhoven, W. van, Halley, D.J., Hout, M.C. van den, Hove, S. van, Johansson, L.F., Jongbloed, J.D., Kamps, R., Kockx, C.E., Koning, B. de, Kriek, M., Deprez, R.L., Lunstroo, H., Mannens, M., Mook, O.R., Nelen, M.R., Ploem, C., Rijnen, M., Saris, J.J., Sinke, R., Sistermans, E., Slegtenhorst, M. van, Sleutels, F., Stoep, N. van der, Tienhoven, M. van, Vermaat, M., Vogel, M., Waisfisz, Q., Weiss, J.M., Wijngaard, A. van den, Workum, W. van, IJntema, H., Zwaag, B. van der, van, I.W.F., Dunnen, J.T. den, Veltman, J.A., Hennekam, R., and Cuppen, E.

Abstract

Item does not contain fulltext

Published
2015

30. Next-generation sequencing-based genome diagnostics across clinical genetics centers: Implementation choices and their effects

Author

Vrijenhoek, T. (T.), Kraaijeveld, K. (Ken), Elferink, M.G. (Martin), Ligt, J. (Joep) de, Kranendonk, E. (Elcke), Santen, G.W.E. (Gijs), Nijman, I.J. (Isaac ), Butler, D. (Derek), Claes, G. (Godelieve), Costessi, A. (Adalberto), Dorlijn, W. (Wim), Van Eyndhoven, W. (Winfried), Halley, D.J.J. (Dicky), Van Den Hout, M.C.G.N. (Mirjam C.G.N.), Van Hove, S. (Steven), Johansson, L.F. (Lennart F.), Jongbloed, J.D.H. (Jan), Kamps, R. (Rick), Kockx, C. (Christel), De Koning, B. (Bart), Kriek, N. (Nadia), Lekanne Dit Deprez, R.H., Lunstroo, H. (Hans), Mannens, M.M.A.M. (Marcel), Mook, O. (Olaf), Nelen, M.R. (Marcel), Ploem, C. (Corrette), Rijnen, M. (Marco), Saris, J.J. (Jasper), Sinke, R.J. (Richard J), Sistermans, E. (Erik), Slegtenhorst, M.A. (Marjon) van, Sleutels, F. (Frank), Stoep, N. (Nienke) van der, Tienhoven, M. (Marianne) van, Vermaat, M. (Martijn), Vogel, M.J. (Maartje), Waisfisz, Q. (Quinten), Weiss, J.M. (Janneke), Wijngaard, A. (Arthur) van den, Workum, W. (W) van, Ijntema, H. (Helger), Zwaag, B. (Bert) van der, IJcken, W.F.J. (Wilfred) van, Dunnen, J.T. (Johan) den, Veltman, J.A. (Joris), Hennekam, R.C.M. (Raoul), Cuppen, E. (Edwin), Vrijenhoek, T. (T.), Kraaijeveld, K. (Ken), Elferink, M.G. (Martin), Ligt, J. (Joep) de, Kranendonk, E. (Elcke), Santen, G.W.E. (Gijs), Nijman, I.J. (Isaac ), Butler, D. (Derek), Claes, G. (Godelieve), Costessi, A. (Adalberto), Dorlijn, W. (Wim), Van Eyndhoven, W. (Winfried), Halley, D.J.J. (Dicky), Van Den Hout, M.C.G.N. (Mirjam C.G.N.), Van Hove, S. (Steven), Johansson, L.F. (Lennart F.), Jongbloed, J.D.H. (Jan), Kamps, R. (Rick), Kockx, C. (Christel), De Koning, B. (Bart), Kriek, N. (Nadia), Lekanne Dit Deprez, R.H., Lunstroo, H. (Hans), Mannens, M.M.A.M. (Marcel), Mook, O. (Olaf), Nelen, M.R. (Marcel), Ploem, C. (Corrette), Rijnen, M. (Marco), Saris, J.J. (Jasper), Sinke, R.J. (Richard J), Sistermans, E. (Erik), Slegtenhorst, M.A. (Marjon) van, Sleutels, F. (Frank), Stoep, N. (Nienke) van der, Tienhoven, M. (Marianne) van, Vermaat, M. (Martijn), Vogel, M.J. (Maartje), Waisfisz, Q. (Quinten), Weiss, J.M. (Janneke), Wijngaard, A. (Arthur) van den, Workum, W. (W) van, Ijntema, H. (Helger), Zwaag, B. (Bert) van der, IJcken, W.F.J. (Wilfred) van, Dunnen, J.T. (Johan) den, Veltman, J.A. (Joris), Hennekam, R.C.M. (Raoul), and Cuppen, E. (Edwin)

Abstract

Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patients with cardiomyopathy. We highlight critical implementation choices, including the specific contributions of laboratory and medical specialists, bioinformaticians and researchers to diagnostic genome care, and how these affect interpretation and reporting of variants. Reported pathogenic mutations were consistent for all but one patient. Of the two centers that were inconsistent in their diagnosis, one reported to have found 'no causal variant', thereby underdiagnosing this patient. The other provided an alternative diagnosis, identifying another variant as causal than the other centers. Ethical and legal analysis showed that informed consent procedures in all centers were generally adequate for diagnostic NGS applications that target a limited set of genes, but not for exome- and genome-based diagnosis. We propose changes to further improve and align these procedures, taking into account the blurring boundary between diagnostics and research, and specific counseling options for exome- and genome-based diagnostics. We conclude that alternative diagnoses may infer a certain level of 'greediness' to come to a positive diagnosis in interpreting sequencing results. Moreover, there is an increasing interdependence of clinic, diagnostics and research departments for comprehensive diagnostic genome care. Therefore, we invite clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care.

Published
2015
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31. Translating sanger-based routine DNA diagnostics into generic massive parallel ion semiconductor sequencing

Author

Diekstra, A., Bosgoed, E.A.J., Rikken, A., Lier, B. van, Kamsteeg, E.J., Tychon, M.W.J., Derks, R.C., Soest, R.A., Mensenkamp, A.R., Scheffer, H., Neveling, K., Nelen, M.R., Diekstra, A., Bosgoed, E.A.J., Rikken, A., Lier, B. van, Kamsteeg, E.J., Tychon, M.W.J., Derks, R.C., Soest, R.A., Mensenkamp, A.R., Scheffer, H., Neveling, K., and Nelen, M.R.

Abstract

Contains fulltext : 154338.pdf (publisher's version ) (Closed access), BACKGROUND: Dideoxy-based chain termination sequencing developed by Sanger is the gold standard sequencing approach and allows clinical diagnostics of disorders with relatively low genetic heterogeneity. Recently, new next generation sequencing (NGS) technologies have found their way into diagnostic laboratories, enabling the sequencing of large targeted gene panels or exomes. The development of benchtop NGS instruments now allows the analysis of single genes or small gene panels, making these platforms increasingly competitive with Sanger sequencing. METHODS: We developed a generic automated ion semiconductor sequencing work flow that can be used in a clinical setting and can serve as a substitute for Sanger sequencing. Standard amplicon-based enrichment remained identical to PCR for Sanger sequencing. A novel postenrichment pooling strategy was developed, limiting the number of library preparations and reducing sequencing costs up to 70% compared to Sanger sequencing. RESULTS: A total of 1224 known pathogenic variants were analyzed, yielding an analytical sensitivity of 99.92% and specificity of 99.99%. In a second experiment, a total of 100 patient-derived DNA samples were analyzed using a blind analysis. The results showed an analytical sensitivity of 99.60% and specificity of 99.98%, comparable to Sanger sequencing. CONCLUSIONS: Ion semiconductor sequencing can be a first choice mutation scanning technique, independent of the genes analyzed.

Published
2015

32. Association of PHB 1630 C > T and MTHFR 677 C > T polymorphisms with breast and ovarian cancer risk in BRCA1/2 mutation carriers: results from a multicenter study

Author

Jakubowska, A., Rozkrut, D., Antoniou, A., Hamann, U., Scott, R.J., McGuffog, L., Healy, S., Sinilnikova, O.M., Rennert, G., Lejbkowicz, F., Flugelman, A., Andrulis, I.L., Glendon, G., Ozcelik, H., Thomassen, M., Paligo, M., Aretini, P., Kantala, J., Aroer, B., Wachenfeldt, A. von, Liljegren, A., Loman, N., Herbst, K., Kristoffersson, U., Rosenquist, R., Karlsson, P., Stenmark-Askmalm, M., Melin, B., Nathanson, K.L., Domchek, S.M., Byrski, T., Huzarski, T., Gronwald, J., Menkiszak, J., Cybulski, C., Serrano, P., Osorio, A., Cajal, T.R., Tsitlaidou, M., Benitez, J., Gilbert, M., Rookus, M., Aalfs, C.M., Kluijt, I., Boessenkool-Pape, J.L., Meijers-Heijboer, H.E.J., Oosterwijk, J.C., Asperen, C.J. van, Blok, M.J., Nelen, M.R., Ouweland, A.M.W. van den, Seynaeve, C., Luijt, R.B. van der, Devilee, P., Easton, D.F., Peock, S., Frost, D., Platte, R., Ellis, S.D., Fineberg, E., Evans, D.G., Lalloo, F., Eeles, R., Jacobs, C., Adlard, J., Davidson, R., Eccles, D., Cole, T., Cook, J., Godwin, A., Bove, B., Stoppa-Lyonnet, D., Caux-Moncoutier, V., Belotti, M., Tirapo, C., Mazoyer, S., Barjhoux, L., Boutry-Kryza, N., Pujol, P., Coupier, I., Peyrat, J.P., Vennin, P., Muller, D., Fricker, J.P., Venat-Bouvet, L., Johannsson, O., Isaacs, C., Schmutzler, R., Wappenschmidt, B., Meindl, A., Arnold, N., Varon-Mateeva, R., Niederacher, D., Sutter, C., Deissler, H., Preisler-Adams, S., Simard, J., Soucy, P., Durocher, F., Chenevix-Trench, G., Beesley, J., Chen, X., Rebbeck, T., Couch, F., Wang, X., Lindor, N., Fredericksen, Z., Pankratz, V.S., Peterlongo, P., Bonanni, B., Fortuzzi, S., Peissel, B., Szabo, C., Mai, P.L., Loud, J.T., Lubinski, J., OCGN, SWE BRCA, HEBON, EMBRACE, GEMO Study Collaborators, KConFab, CIMBA, Damage and Repair in Cancer Development and Cancer Treatment (DARE), Targeted Gynaecologic Oncology (TARGON), Human Genetics, CCA -Cancer Center Amsterdam, ARD - Amsterdam Reproduction and Development, Genetica & Celbiologie, Klinische Genetica, RS: GROW - School for Oncology and Reproduction, Clinical Genetics, Medical Oncology, IHS, Human genetics, and CCA - Oncogenesis

Subjects
Oncology, Cancer Research, endocrine system diseases, BRCA1/2 mutation carriers, METHYLENETETRAHYDROFOLATE REDUCTASE MTHFR, Genes, BRCA2, Genes, BRCA1, DCN PAC - Perception action and control, SUSCEPTIBILITY, medicine.disease_cause, Bioinformatics, T+polymorphism%22">PHB 1630 C>T polymorphism, 0302 clinical medicine, PROHIBITIN 3'-UNTRANSLATED REGION, Genotype, Prohibitin, skin and connective tissue diseases, breast/ovarian cancer risk, Ovarian Neoplasms, 0303 health sciences, FOLATE STATUS, CARCINOGENESIS, Penetrance, 3. Good health, 030220 oncology & carcinogenesis, Female, +T+polymorphism%22">PHB 1630 C > T polymorphism, CHROMOSOME-17, Risk, EXPRESSION, medicine.medical_specialty, Heterozygote, Hereditary cancer and cancer-related syndromes Genetics and epigenetic pathways of disease [ONCOL 1], Breast Neoplasms, +T+polymorphism%22">MTHFR 677 C > T polymorphism, Biology, Genomic disorders and inherited multi-system disorders [IGMD 3], 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Translational research [ONCOL 3], Internal medicine, Prohibitins, medicine, Humans, Genetic Predisposition to Disease, Genetics and epigenetic pathways of disease Translational research [NCMLS 6], Methylenetetrahydrofolate Reductase (NADPH2), 030304 developmental biology, Polymorphism, Genetic, Hereditary cancer and cancer-related syndromes [ONCOL 1], Biology and Life Sciences, Genetics and Genomics, medicine.disease, GENE, Minor allele frequency, Repressor Proteins, COMMON MUTATION, T+polymorphism%22">MTHFR 677 C>T polymorphism, Methylenetetrahydrofolate reductase, Mutation, biology.protein, RNA, Carcinogenesis, Ovarian cancer
Abstract

BACKGROUND: The variable penetrance of breast cancer in BRCA1/2 mutation carriers suggests that other genetic or environmental factors modify breast cancer risk. Two genes of special interest are prohibitin (PHB) and methylene-tetrahydrofolate reductase (MTHFR), both of which are important either directly or indirectly in maintaining genomic integrity.METHODS: To evaluate the potential role of genetic variants within PHB and MTHFR in breast and ovarian cancer risk, 4102 BRCA1 and 2093 BRCA2 mutation carriers, and 6211 BRCA1 and 2902 BRCA2 carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA) were genotyped for the PHB 1630 C>T (rs6917) polymorphism and the MTHFR 677 C>T (rs1801133) polymorphism, respectively.RESULTS: There was no evidence of association between the PHB 1630 C>T and MTHFR 677 C>T polymorphisms with either disease for BRCA1 or BRCA2 mutation carriers when breast and ovarian cancer associations were evaluated separately. Analysis that evaluated associations for breast and ovarian cancer simultaneously showed some evidence that BRCA1 mutation carriers who had the rare homozygote genotype (TT) of the PHB 1630 C>T polymorphism were at increased risk of both breast and ovarian cancer (HR 1.50, 95% CI 1.10-2.04 and HR 2.16, 95% CI 1.24-3.76, respectively). However, there was no evidence of association under a multiplicative model for the effect of each minor allele.CONCLUSION: The PHB 1630TT genotype may modify breast and ovarian cancer risks in BRCA1 mutation carriers. This association need to be evaluated in larger series of BRCA1 mutation carriers. British Journal of Cancer (2012) 106, 2016-2024. doi:10.1038/bjc.2012.160 www.bjcancer.com Published online 15 May 2012 (C) 2012 Cancer Research UK

Published
2012

33. Evidence for SMAD3 as a modifier of breast cancer risk in BRCA2 mutation carriers

Author

Walker, L.C., Fredericksen, Z.S., Wang, X.S., Tarrell, R., Pankratz, V.S., Lindor, N.M., Beesley, J., Healey, S., Chen, X.Q., Fab, K.C., Stoppa-Lyonnet, D., Tirapo, C., Giraud, S., Mazoyer, S., Muller, D., Fricker, J.P., Delnatte, C., Schmutzler, R.K., Wappenschmidt, B., Engel, C., Schonbuchner, I., Deissler, H., Meindl, A., Hogervorst, F.B., Verheus, M., Hooning, M.J., Ouweland, A.M.W. van den, Nelen, M.R., Ausems, M.G.E.M., Aalfs, C.M., Asperen, C.J. van, Devilee, P., Gerrits, M.M., Waisfisz, Q., Szabo, C.I., Quad, M.S., Easton, D.F., Peock, S., Cook, M., Oliver, C.T., Frost, D., Harrington, P., Evans, D.G., Lalloo, F., Eeles, R., Izatt, L., Chu, C., Davidson, R., Eccles, D., Ong, K.R., Cook, J., Rebbeck, T., Nathanson, K.L., Domchek, S.M., Singer, C.F., Gschwantler-Kaulich, D., Dressler, A.C., Pfeiler, G., Godwin, A.K., Heikkinen, T., Nevanlinna, H., Agnarsson, B.A., Caligo, M.A., Olsson, H., Kristoffersson, U., Liljegren, A., Arver, B., Karlsson, P., Melin, B., Sinilnikova, O.M., McGuffog, L., Antoniou, A.C., Chenevix-Trench, G., Spurdle, A.B., Couch, F.J., Gemo Study Collaborators, HEBON, EMBRACE, SWE BRCA, Easton, Douglas [0000-0003-2444-3247], Antoniou, Antonis [0000-0001-9223-3116], Apollo - University of Cambridge Repository, Division of Genetics and Population Health, Queensland Institute of Medical Research, Department of Laboratory Medicine and Pathology, Mayo Clinic, Pathologie moléculaire des cancers, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Centre Léon Bérard [Lyon]-Hospices Civils de Lyon (HCL), Génétique moléculaire, signalisation et cancer (GMSC), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Unité d'Oncogénétique, CLCC Paul Strauss, Centre René Gauducheau, Centre for Hereditary Breast and Ovarian Cancer, Department of Obstetrics and Gynaecology-University of Cologne, Institute for Medical Informatics, Statistics and Epidemiology [Leipzig] (IMISE), Universität Leipzig [Leipzig], Institute of Human Genetics, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Department of Obstetrics and Gynaecology, Universität Ulm - Ulm University [Ulm, Allemagne], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)-Klinikum Rechts der Isar-Division of Tumor Genetics, Family Cancer Clinic, The Netherlands Cancer Institute, Department of Epidemiology, Netherlands Cancer Institute, Department of Medical Oncology, Erasmus University Medical Center [Rotterdam] (Erasmus MC)-Family Cancer Clinic, Department of Clinical Genetics, Department of Human Genetics, University Nijmegen Medical Centre, Department of Medical Genetics, University Medical Center [Utrecht], Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA), Leiden University Medical Center (LUMC), Department of Human Genetics & Department of Pathology, Department of Genetics and Cell Biology, VU University Medical Center [Amsterdam], Strangeways Research Laboratory, University of Cambridge [UK] (CAM)-Department of Public Health and Primary Care-Centre for Cancer Genetic Epidemiology, Centre for Cancer Genetic Epidemiology [Cambridge], Department of Oncology-University of Cambridge [UK] (CAM), Genetic Medicine, St Mary's Hospital-NHS Foundation Trust-Manchester Academic Health Sciences Centre-Central Manchester University Hospitals, Oncogenetics Team, The Institute of Cancer Research-Royal Marsden NHS Foundation Trust, Clinical Genetics Department, Guy's and St Thomas NHS Foundation Trust-Guys Hospital, Yorkshire Regional Genetics Service, St. James's Hospital, Ferguson-Smith Centre for Clinical Genetics, Wessex Clinical Genetics Service, Princess Anne Hospital-Cancer Sciences Division, West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania [Philadelphia]-University of Pennsylvania [Philadelphia], Division of Special Gynecology, Medizinische Universität Wien = Medical University of Vienna-Department of OB/GYN, Women's Cancer Program, Fox Chase Cancer Center, Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Department of Pathology, University Hospital and University of Iceland School of Medicine, Section of Genetic Oncology, University of Pisa - Università di Pisa, Department of Oncology, Lund University Hospital, Karolinska University Hospital [Stockholm], Sahlgrenska University Hospital [Gothenburg], Department of Radiation Sciences and Oncology, Umeå University, kConFab, GEMO Study Collaborators, HEBON, ModSQuaD, EMBRACE, SWE-BRCA, Human Genetics, BMC, Ed., Julius-Maximilians-Universität Würzburg (JMU), University of Cambridge [UK] (CAM)-Department of Oncology, University of Pennsylvania-University of Pennsylvania, Medical Oncology, Clinical Genetics, Gastroenterology & Hepatology, Targeted Gynaecologic Oncology (TARGON), and Damage and Repair in Cancer Development and Cancer Treatment (DARE)

Subjects
MESH: Signal Transduction, Linkage disequilibrium, Candidate gene, endocrine system diseases, Genes, BRCA2, Gene Expression, Genome-wide association study, Gene mutation, Linkage Disequilibrium, 0302 clinical medicine, MESH: Aged, 80 and over, MESH: Risk Factors, Risk Factors, Transforming Growth Factor beta, INVESTIGATORS, skin and connective tissue diseases, POPULATION, Medicine(all), Genetics, MESH: Aged, Aged, 80 and over, 0303 health sciences, MESH: Middle Aged, MESH: Polymorphism, Single Nucleotide, MESH: Genetic Predisposition to Disease, Middle Aged, BRCA2 Protein, MESH: Linkage Disequilibrium, 030220 oncology & carcinogenesis, Female, Signal Transduction, Research Article, Adult, MESH: Mutation, MESH: Gene Expression, GENES, Single-nucleotide polymorphism, [SDV.CAN]Life Sciences [q-bio]/Cancer, Breast Neoplasms, Biology, Polymorphism, Single Nucleotide, OVARIAN-CANCER, PROPHYLACTIC OOPHORECTOMY, 03 medical and health sciences, Breast cancer, [SDV.CAN] Life Sciences [q-bio]/Cancer, SDG 3 - Good Health and Well-being, medicine, MESH: Smad3 Protein, Humans, Genetic Predisposition to Disease, COHORT, Smad3 Protein, GENOME-WIDE ASSOCIATION, MESH: Transforming Growth Factor beta, 030304 developmental biology, Genetic association, Aged, MESH: Humans, CONSORTIUM, MESH: Adult, ALLELES, medicine.disease, POLYMORPHISM, Cancer and Oncology, MESH: Genome-Wide Association Study, Mutation, MESH: Female, MESH: Breast Neoplasms, MESH: Genes, BRCA2, Genome-Wide Association Study
Abstract

Introduction: Current attempts to identify genetic modifiers of BRCA1 and BRCA2 associated risk have focused on a candidate gene approach, based on knowledge of gene functions, or the development of large genome-wide association studies. In this study, we evaluated 24 SNPs tagged to 14 candidate genes derived through a novel approach that analysed gene expression differences to prioritise candidate modifier genes for association studies.Methods: We successfully genotyped 24 SNPs in a cohort of up to 4,724 BRCA1 and 2,693 BRCA2 female mutation carriers from 15 study groups and assessed whether these variants were associated with risk of breast cancer in BRCA1 and BRCA2 mutation carriers.Results: SNPs in five of the 14 candidate genes showed evidence of association with breast cancer risk for BRCA1 or BRCA2 carriers (P Conclusions: This study provides evidence that the SMAD3 gene, which encodes a key regulatory protein in the transforming growth factor beta signalling pathway and is known to interact directly with BRCA2, may contribute to increased risk of breast cancer in BRCA2 mutation carriers. This finding suggests that genes with expression associated with BRCA1 and BRCA2 mutation status are enriched for the presence of common genetic modifiers of breast cancer risk in these populations.

Published
2010

34. A post-hoc comparison of the utility of sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases

Author

Neveling, K., Feenstra, I., Gilissen, C., Hoefsloot, L.H., Kamsteeg, E.J., Mensenkamp, A.R., Rodenburg, R.J.T., Yntema, H.G., Spruijt, L., Vermeer, S., Rinne, T., Gassen, K.L.I. van, Bodmer, D., Lugtenberg, D., Reuver, R. de, Buijsman, W., Derks, R.C., Wieskamp, N., Heuvel, B. van den, Ligtenberg, M.J.L., Kremer, H., Koolen, D.A., Warrenburg, B.P.C. van de, Cremers, F.P.M., Marcelis, C.L.M., Smeitink, J.A.M., Wortmann, S.B., Zelst-Stams, W.A.G. van, Veltman, J.A., Brunner, H.G., Scheffer, H., Nelen, M.R., Neveling, K., Feenstra, I., Gilissen, C., Hoefsloot, L.H., Kamsteeg, E.J., Mensenkamp, A.R., Rodenburg, R.J.T., Yntema, H.G., Spruijt, L., Vermeer, S., Rinne, T., Gassen, K.L.I. van, Bodmer, D., Lugtenberg, D., Reuver, R. de, Buijsman, W., Derks, R.C., Wieskamp, N., Heuvel, B. van den, Ligtenberg, M.J.L., Kremer, H., Koolen, D.A., Warrenburg, B.P.C. van de, Cremers, F.P.M., Marcelis, C.L.M., Smeitink, J.A.M., Wortmann, S.B., Zelst-Stams, W.A.G. van, Veltman, J.A., Brunner, H.G., Scheffer, H., and Nelen, M.R.

Abstract

Contains fulltext : 124810.pdf (publisher's version ) (Closed access), The advent of massive parallel sequencing is rapidly changing the strategies employed for the genetic diagnosis and research of rare diseases that involve a large number of genes. So far it is not clear whether these approaches perform significantly better than conventional single gene testing as requested by clinicians. The current yield of this traditional diagnostic approach depends on a complex of factors that include gene-specific phenotype traits, and the relative frequency of the involvement of specific genes. To gauge the impact of the paradigm shift that is occurring in molecular diagnostics, we assessed traditional Sanger-based sequencing (in 2011) and exome sequencing followed by targeted bioinformatics analysis (in 2012) for five different conditions that are highly heterogeneous, and for which our center provides molecular diagnosis. We find that exome sequencing has a much higher diagnostic yield than Sanger sequencing for deafness, blindness, mitochondrial disease, and movement disorders. For microsatellite-stable colorectal cancer, this was low under both strategies. Even if all genes that could have been ordered by physicians had been tested, the larger number of genes captured by the exome would still have led to a clearly superior diagnostic yield at a fraction of the cost.

Published
2013

35. Association of PHB 1630 C>T and MTHFR 677 C>T polymorphisms with breast and ovarian cancer risk in BRCA1/2 mutation carriers: results from a multicenter study.

Author

Jakubowska, A., Rozkrut, D., Antoniou, A., Hamann, U., Scott, R.J., McGuffog, L., Healy, S., Sinilnikova, O.M., Rennert, G., Lejbkowicz, F., Flugelman, A., Andrulis, I.L., Glendon, G., Ozcelik, H., Thomassen, M., Paligo, M., Aretini, P., Kantala, J., Aroer, B., Wachenfeldt, A. von, Liljegren, A., Loman, N., Herbst, K., Kristoffersson, U., Rosenquist, R., Karlsson, P., Stenmark-Askmalm, M., Melin, B., Nathanson, K.L., Domchek, S.M., Byrski, T., Huzarski, T., Gronwald, J., Menkiszak, J., Cybulski, C., Serrano, P., Osorio, A., Cajal, T.R., Tsitlaidou, M., Benitez, J., Gilbert, M., Rookus, M., Aalfs, C.M., Kluijt, I., Boessenkool-Pape, J.L., Meijers-Heijboer, H.E., Oosterwijk, J.C., Asperen, C.J. van, Blok, M.J., Nelen, M.R., Ouweland, A.M. van den, Seynaeve, C., Luijt, R.B. van der, Devilee, P., Easton, D.F., Peock, S., Frost, D., Platte, R., Ellis, S.D., Fineberg, E., Evans, D.G., Lalloo, F., Eeles, R., Jacobs, C, Adlard, J., Davidson, R., Eccles, D., Cole, T., Cook, J.L., Godwin, A., Bove, B., Stoppa-Lyonnet, D., Caux-Moncoutier, V., Belotti, M., Tirapo, C., Mazoyer, S., Barjhoux, L., Boutry-Kryza, N., Pujol, P., Coupier, I., Peyrat, J.P., Vennin, P., Muller, D., Fricker, J.P., Venat-Bouvet, L., Johannsson, O.T., Isaacs, C., Schmutzler, R., Wappenschmidt, B., Meindl, A., Arnold, N., Varon-Mateeva, R., Niederacher, D., Sutter, C., Deissler, H., Preisler-Adams, S., Simard, J., Soucy, P., Durocher, F., Chenevix-Trench, G., Beesley, J., Chen, X., Rebbeck, T., Couch, F., Wang, X., Lindor, N., Fredericksen, Z., Pankratz, V.S., Peterlongo, P., Bonanni, B., Fortuzzi, S., Peissel, B., Szabo, C., Mai, P.L., Loud, J.T., Lubinski, J., Ligtenberg, M.J.L., Hoogerbrugge, N., et al., Jakubowska, A., Rozkrut, D., Antoniou, A., Hamann, U., Scott, R.J., McGuffog, L., Healy, S., Sinilnikova, O.M., Rennert, G., Lejbkowicz, F., Flugelman, A., Andrulis, I.L., Glendon, G., Ozcelik, H., Thomassen, M., Paligo, M., Aretini, P., Kantala, J., Aroer, B., Wachenfeldt, A. von, Liljegren, A., Loman, N., Herbst, K., Kristoffersson, U., Rosenquist, R., Karlsson, P., Stenmark-Askmalm, M., Melin, B., Nathanson, K.L., Domchek, S.M., Byrski, T., Huzarski, T., Gronwald, J., Menkiszak, J., Cybulski, C., Serrano, P., Osorio, A., Cajal, T.R., Tsitlaidou, M., Benitez, J., Gilbert, M., Rookus, M., Aalfs, C.M., Kluijt, I., Boessenkool-Pape, J.L., Meijers-Heijboer, H.E., Oosterwijk, J.C., Asperen, C.J. van, Blok, M.J., Nelen, M.R., Ouweland, A.M. van den, Seynaeve, C., Luijt, R.B. van der, Devilee, P., Easton, D.F., Peock, S., Frost, D., Platte, R., Ellis, S.D., Fineberg, E., Evans, D.G., Lalloo, F., Eeles, R., Jacobs, C, Adlard, J., Davidson, R., Eccles, D., Cole, T., Cook, J.L., Godwin, A., Bove, B., Stoppa-Lyonnet, D., Caux-Moncoutier, V., Belotti, M., Tirapo, C., Mazoyer, S., Barjhoux, L., Boutry-Kryza, N., Pujol, P., Coupier, I., Peyrat, J.P., Vennin, P., Muller, D., Fricker, J.P., Venat-Bouvet, L., Johannsson, O.T., Isaacs, C., Schmutzler, R., Wappenschmidt, B., Meindl, A., Arnold, N., Varon-Mateeva, R., Niederacher, D., Sutter, C., Deissler, H., Preisler-Adams, S., Simard, J., Soucy, P., Durocher, F., Chenevix-Trench, G., Beesley, J., Chen, X., Rebbeck, T., Couch, F., Wang, X., Lindor, N., Fredericksen, Z., Pankratz, V.S., Peterlongo, P., Bonanni, B., Fortuzzi, S., Peissel, B., Szabo, C., Mai, P.L., Loud, J.T., Lubinski, J., Ligtenberg, M.J.L., Hoogerbrugge, N., and et al.

Abstract

Item does not contain fulltext, BACKGROUND: The variable penetrance of breast cancer in BRCA1/2 mutation carriers suggests that other genetic or environmental factors modify breast cancer risk. Two genes of special interest are prohibitin (PHB) and methylene-tetrahydrofolate reductase (MTHFR), both of which are important either directly or indirectly in maintaining genomic integrity. METHODS: To evaluate the potential role of genetic variants within PHB and MTHFR in breast and ovarian cancer risk, 4102 BRCA1 and 2093 BRCA2 mutation carriers, and 6211 BRCA1 and 2902 BRCA2 carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA) were genotyped for the PHB 1630 C>T (rs6917) polymorphism and the MTHFR 677 C>T (rs1801133) polymorphism, respectively. RESULTS: There was no evidence of association between the PHB 1630 C>T and MTHFR 677 C>T polymorphisms with either disease for BRCA1 or BRCA2 mutation carriers when breast and ovarian cancer associations were evaluated separately. Analysis that evaluated associations for breast and ovarian cancer simultaneously showed some evidence that BRCA1 mutation carriers who had the rare homozygote genotype (TT) of the PHB 1630 C>T polymorphism were at increased risk of both breast and ovarian cancer (HR 1.50, 95%CI 1.10-2.04 and HR 2.16, 95%CI 1.24-3.76, respectively). However, there was no evidence of association under a multiplicative model for the effect of each minor allele. CONCLUSION: The PHB 1630TT genotype may modify breast and ovarian cancer risks in BRCA1 mutation carriers. This association need to be evaluated in larger series of BRCA1 mutation carriers.

Published
2012

36. Genome and exome sequencing in the clinic: unbiased genomic approaches with a high diagnostic yield

Author

Nelen, M.R., Veltman, J.A., Nelen, M.R., and Veltman, J.A.

Abstract

Item does not contain fulltext, For the reasons discussed here, we think whole-genome- or exome-based approaches are currently most suited for diagnostic implementation in genetically heterogeneous diseases, initially to complement and later to replace Sanger sequencing, qPCR and genomic microarrays. Patients do need to be counseled for the possibility of receiving medically relevant information not related to the disease under investigation, but this chance can be minimized by a focused data-analysis process. Establishing the pathogenicity of individual genetic variants remains a daunting task, requiring novel bioinformatic tools and high-throughput functional approaches, but at least we can now be more sure that we have not missed relevant genetic variation.

Published
2012

37. Association of PHB 1630 C>T and MTHFR 677 C>T polymorphisms with breast and ovarian cancer risk in BRCA1/2 mutation carriers: Results from a multicenter study

Author

Jakubowska, A. (Anna), Rozkrut, D. (D.), Antoniou, A.C. (Antonis), Hamann, U. (Ute), Scott, R.J. (Rodney), McGuffog, L. (Lesley), Healy, S. (S.), Sinilnikova, O. (Olga), Rennert, G. (Gad), Lejbkowicz, F. (Flavio), Flugelman, A. (Anath), Andrulis, I.L. (Irene), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Thomassen, M. (Mads), Paligo, M. (M.), Aretini, P. (Paolo), Kantala, J. (J.), Aroer, B. (B.), Wachenfeldt, A. (Anna) von, Liljegren, A. (Annelie), Loman, N. (Niklas), Herbst, H., Kristoffersson, U. (Ulf), Rosenquist, R. (R.), Karlsson, P. (Per), Stenmark-Askmalm, M. (M.), Melin, B. (Beatrice), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Byrski, T. (Tomasz), Huzarski, T. (Tomasz), Gronwald, J. (Jacek), Menkiszak, J. (Janusz), Cybulski, C. (Cezary), Serrano, P. (Pedro), Osorio, A. (Ana), Cajal, T.R., Tsitlaidou, M. (M.), Benítez, J. (Javier), Gilbert, M. (Michel), Rookus, M.A. (Matti), Aalfs, C.M. (Cora), Kluijt, I. (Irma), Boessenkool-Pape, J.L. (J.), Meijers-Heijboer, E.J. (Hanne), Oosterwijk, J.C. (Jan), Asperen, C.J. (Christi) van, Blok, M.J. (Marinus), Nelen, M.R. (Marcel), Ouweland, A.M.W. (Ans) van den, Seynaeve, C.M. (Caroline), Luijt, R.B. (Rob) van der, Devilee, P. (Peter), Easton, D.F. (Douglas), Peock, S. (Susan), Frost, D. (Debra), Platte, R. (Radka), Ellis, S.D. (Steve), Fineberg, E. (Elena), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Eeles, R. (Rosalind), Jacobs, C. (Chris), Adlard, J.W. (Julian), Davidson, R. (Rosemarie), Eccles, D. (Diana), Cole, T.J. (Trevor), Cook, J. (Jackie), Godwin, A.K. (Andrew), Bove, B. (B.), Stoppa-Lyonnet, D. (Dominique), Caux-Moncoutier, V. (Virginie), Belotti, M. (Muriel), Tirapo, C. (Carole), Mazoyer, S. (Sylvie), Barjhoux, L. (Laure), Boutry-Kryza, N. (N.), Pujol, P. (Pascal), Coupier, I. (Isabelle), Peyrat, J.-P., Vennin, P. (Philippe), Muller, D.W. (Danièle), Fricker, J.P. (Jean Pierre), Vénat-Bouvet, L. (Laurence), Johannson, O.T. (Oskar), Isaacs, C. (Claudine), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Meindl, A. (Alfons), Arnold, N. (Norbert), Varon-Mateeva, R. (Raymonda), Niederacher, D. (Dieter), Sutter, C. (Christian), Deissler, H. (Helmut), Preisler-Adams, S. (Sabine), Simard, J. (Jacques), Soucy, P. (Penny), Durocher, F. (Francine), Chenevix-Trench, G. (Georgia), Beesley, J. (Jonathan), Chen, X.C. (X. C.), Rebbeck, R. (Timothy), Couch, F.J. (Fergus), Wang, X. (Xing), Lindor, N.M. (Noralane), Fredericksen, Z. (Zachary), Pankratz, V.S. (Shane), Peterlongo, P. (Paolo), Bonnani, B. (Bernardo), Fortuzzi, S. (S.), Peissel, B. (Bernard), Szabo, C. (Csilla), Mai, P.L. (Phuong), Loud, J.T. (Jennifer), Lubinski, J. (Jan), Jakubowska, A. (Anna), Rozkrut, D. (D.), Antoniou, A.C. (Antonis), Hamann, U. (Ute), Scott, R.J. (Rodney), McGuffog, L. (Lesley), Healy, S. (S.), Sinilnikova, O. (Olga), Rennert, G. (Gad), Lejbkowicz, F. (Flavio), Flugelman, A. (Anath), Andrulis, I.L. (Irene), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Thomassen, M. (Mads), Paligo, M. (M.), Aretini, P. (Paolo), Kantala, J. (J.), Aroer, B. (B.), Wachenfeldt, A. (Anna) von, Liljegren, A. (Annelie), Loman, N. (Niklas), Herbst, H., Kristoffersson, U. (Ulf), Rosenquist, R. (R.), Karlsson, P. (Per), Stenmark-Askmalm, M. (M.), Melin, B. (Beatrice), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Byrski, T. (Tomasz), Huzarski, T. (Tomasz), Gronwald, J. (Jacek), Menkiszak, J. (Janusz), Cybulski, C. (Cezary), Serrano, P. (Pedro), Osorio, A. (Ana), Cajal, T.R., Tsitlaidou, M. (M.), Benítez, J. (Javier), Gilbert, M. (Michel), Rookus, M.A. (Matti), Aalfs, C.M. (Cora), Kluijt, I. (Irma), Boessenkool-Pape, J.L. (J.), Meijers-Heijboer, E.J. (Hanne), Oosterwijk, J.C. (Jan), Asperen, C.J. (Christi) van, Blok, M.J. (Marinus), Nelen, M.R. (Marcel), Ouweland, A.M.W. (Ans) van den, Seynaeve, C.M. (Caroline), Luijt, R.B. (Rob) van der, Devilee, P. (Peter), Easton, D.F. (Douglas), Peock, S. (Susan), Frost, D. (Debra), Platte, R. (Radka), Ellis, S.D. (Steve), Fineberg, E. (Elena), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Eeles, R. (Rosalind), Jacobs, C. (Chris), Adlard, J.W. (Julian), Davidson, R. (Rosemarie), Eccles, D. (Diana), Cole, T.J. (Trevor), Cook, J. (Jackie), Godwin, A.K. (Andrew), Bove, B. (B.), Stoppa-Lyonnet, D. (Dominique), Caux-Moncoutier, V. (Virginie), Belotti, M. (Muriel), Tirapo, C. (Carole), Mazoyer, S. (Sylvie), Barjhoux, L. (Laure), Boutry-Kryza, N. (N.), Pujol, P. (Pascal), Coupier, I. (Isabelle), Peyrat, J.-P., Vennin, P. (Philippe), Muller, D.W. (Danièle), Fricker, J.P. (Jean Pierre), Vénat-Bouvet, L. (Laurence), Johannson, O.T. (Oskar), Isaacs, C. (Claudine), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Meindl, A. (Alfons), Arnold, N. (Norbert), Varon-Mateeva, R. (Raymonda), Niederacher, D. (Dieter), Sutter, C. (Christian), Deissler, H. (Helmut), Preisler-Adams, S. (Sabine), Simard, J. (Jacques), Soucy, P. (Penny), Durocher, F. (Francine), Chenevix-Trench, G. (Georgia), Beesley, J. (Jonathan), Chen, X.C. (X. C.), Rebbeck, R. (Timothy), Couch, F.J. (Fergus), Wang, X. (Xing), Lindor, N.M. (Noralane), Fredericksen, Z. (Zachary), Pankratz, V.S. (Shane), Peterlongo, P. (Paolo), Bonnani, B. (Bernardo), Fortuzzi, S. (S.), Peissel, B. (Bernard), Szabo, C. (Csilla), Mai, P.L. (Phuong), Loud, J.T. (Jennifer), and Lubinski, J. (Jan)

Abstract

Background: The variable penetrance of breast cancer in BRCA1/2 mutation carriers suggests that other genetic or environmental factors modify breast cancer risk. Two genes of special interest are prohibitin (PHB) and methylene-tetrahydrofolate reductase (MTHFR), both of which are important either directly or indirectly in maintaining genomic integrity. Methods: To evaluate the potential role of genetic variants within PHB and MTHFR in breast and ovarian cancer risk, 4102 BRCA1 and 2093 BRCA2 mutation carriers, and 6211 BRCA1 and 2902 BRCA2 carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA) were genotyped for the PHB 1630 C>T (rs6917) polymorphism and the MTHFR 677 C>T (rs1801133) polymorphism, respectively. Results: There was no evidence of association between the PHB 1630 C>T and MTHFR 677 C>T polymorphisms with either disease for BRCA1 or BRCA2 mutation carriers when breast and ovarian cancer associations were evaluated separately. Analysis that evaluated associations for breast and ovarian cancer simultaneously showed some evidence that BRCA1 mutation carriers who had the rare homozygote genotype (TT) of the PHB 1630 C>T polymorphism were at increased risk of both breast and ovarian cancer (HR 1.50, 95%CI 1.10-2.04 and HR 2.16, 95%CI 1.24-3.76, respectively). However, there was no evidence of association under a multiplicative model for the effect of each minor allele. Conclusion: The PHB 1630TT genotype may modify breast and ovarian cancer risks in BRCA1 mutation carriers. This association need to be evaluated in larger series of BRCA1 mutation carriers.

Published
2012
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38. Characterization of a novel transcript of the EHMT1 gene reveals important diagnostic implications for Kleefstra syndrome

Author

Nillesen, W.M., Yntema, H.G., Moscarda, M., Verbeek, N.E., Wilson, L.C., Cowan, F., Schepens, M., Raas-Rothschild, A., Gafni-Weinstein, O., Zollino, M., Vijzelaar, R., Neri, G., Nelen, M.R., Bokhoven, J.H.L.M. van, Giltay, J., Kleefstra, T., Nillesen, W.M., Yntema, H.G., Moscarda, M., Verbeek, N.E., Wilson, L.C., Cowan, F., Schepens, M., Raas-Rothschild, A., Gafni-Weinstein, O., Zollino, M., Vijzelaar, R., Neri, G., Nelen, M.R., Bokhoven, J.H.L.M. van, Giltay, J., and Kleefstra, T.

Abstract

Contains fulltext : 95713.pdf (publisher's version ) (Closed access), The core phenotype of Kleefstra syndrome (KS) is characterized by intellectual disability, childhood hypotonia, and a characteristic facial appearance. This can be caused by either submicroscopic 9q34 deletions or loss of function mutations of the EHMT1 gene. Remarkably, in three patients with a clinical suspicion of KS, molecular cytogenetic analysis revealed an interstitial 9q34 microdeletion proximal to the coding region of the EHMT1 gene based on the NM_ 024757.3 transcript. Because we found a mono-allelic EHMT1 transcript suggestive for haploinsufficiency of EHMT1 in two of these patients tested, we hypothesized that a deletion of regulatory elements or so far unknown coding sequences in the 5' region of the EHMT1 gene, might result in a phenotype compatible with KS. We further characterized the molecular content of deletions proximal to the transcript NM_ 024757.3 and confirmed presence of a novel predicted open reading frame comprising 27 coding exons (NM_ 024757.4). Further analysis showed that all three deletions included the presumed novel first exon of the EHMT1 gene. Subsequent testing of 75 individuals without previously detectable EHMT1 aberrations showed one additional case with a deletion comprising only this 5' part of the gene. These results have important implications for the genetic screening of KS and for studies of the functional significance of EHMT1.

Published
2011

39. Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2

Author

Mulligan, A.M., Couch, F.J., Barrowdale, D., Domchek, S.M., Eccles, D., Nevanlinna, H., Ramus, S.J., Robson, M., Sherman, M., Spurdle, A.B., Wappenschmidt, B., Lee, A., McGuffog, L., Healey, S., Sinilnikova, O.M., Janavicius, R., Hansen, T.V., Nielsen, F.C., Ejlertsen, B., Osorio, A., Munoz-Repeto, I., Duran, M., Godino, J., Pertesi, M., Benitez, J., Peterlongo, P., Manoukian, S., Peissel, B., Zaffaroni, D., Cattaneo, E., Bonanni, B., Viel, A., Pasini, B., Papi, L., Ottini, L., Savarese, A., Bernard, L., Radice, P., Hamann, U., Verheus, M., Meijers-Heijboer, H.E., Wijnen, J., Gomez Garcia, E.B., Nelen, M.R., Kets, C.M., Seynaeve, C., Tilanus-Linthorst, M.M., Luijt, R.B. van der, Os, T.V., Rookus, M., Frost, D., Jones, J.L., Evans, D.G., Lalloo, F., Eeles, R., Izatt, L., Adlard, J., Davidson, R., Cook, J., Donaldson, A., Dorkins, H., Gregory, H., Eason, J., Houghton, C., Barwell, J., Side, L.E., McCann, E., Murray, A., Peock, S., Godwin, A.K., Schmutzler, R.K., Rhiem, K., Engel, C., Meindl, A., Ruehl, I., Arnold, N., Niederacher, D., Sutter, C., Deissler, H., Gadzicki, D., Kast, K., Preisler-Adams, S., Varon-Mateeva, R., Schoenbuchner, I., Fiebig, B., Heinritz, W., Schafer, D., Gevensleben, H., Caux-Moncoutier, V., Fassy-Colcombet, M., Cornelis, F., Mazoyer, S., Leone, M., Boutry-Kryza, N., Hardouin, A., Berthet, P., Muller, D., Fricker, J.P., Mortemousque, I., Pujol, P., et al., Mulligan, A.M., Couch, F.J., Barrowdale, D., Domchek, S.M., Eccles, D., Nevanlinna, H., Ramus, S.J., Robson, M., Sherman, M., Spurdle, A.B., Wappenschmidt, B., Lee, A., McGuffog, L., Healey, S., Sinilnikova, O.M., Janavicius, R., Hansen, T.V., Nielsen, F.C., Ejlertsen, B., Osorio, A., Munoz-Repeto, I., Duran, M., Godino, J., Pertesi, M., Benitez, J., Peterlongo, P., Manoukian, S., Peissel, B., Zaffaroni, D., Cattaneo, E., Bonanni, B., Viel, A., Pasini, B., Papi, L., Ottini, L., Savarese, A., Bernard, L., Radice, P., Hamann, U., Verheus, M., Meijers-Heijboer, H.E., Wijnen, J., Gomez Garcia, E.B., Nelen, M.R., Kets, C.M., Seynaeve, C., Tilanus-Linthorst, M.M., Luijt, R.B. van der, Os, T.V., Rookus, M., Frost, D., Jones, J.L., Evans, D.G., Lalloo, F., Eeles, R., Izatt, L., Adlard, J., Davidson, R., Cook, J., Donaldson, A., Dorkins, H., Gregory, H., Eason, J., Houghton, C., Barwell, J., Side, L.E., McCann, E., Murray, A., Peock, S., Godwin, A.K., Schmutzler, R.K., Rhiem, K., Engel, C., Meindl, A., Ruehl, I., Arnold, N., Niederacher, D., Sutter, C., Deissler, H., Gadzicki, D., Kast, K., Preisler-Adams, S., Varon-Mateeva, R., Schoenbuchner, I., Fiebig, B., Heinritz, W., Schafer, D., Gevensleben, H., Caux-Moncoutier, V., Fassy-Colcombet, M., Cornelis, F., Mazoyer, S., Leone, M., Boutry-Kryza, N., Hardouin, A., Berthet, P., Muller, D., Fricker, J.P., Mortemousque, I., Pujol, P., and et al.

Abstract

Contains fulltext : 97737.pdf (publisher's version ) (Open Access), INTRODUCTION: Previous studies have demonstrated that common breast cancer susceptibility alleles are differentially associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. It is currently unknown how these alleles are associated with different breast cancer subtypes in BRCA1 and BRCA2 mutation carriers defined by estrogen (ER) or progesterone receptor (PR) status of the tumour. METHODS: We used genotype data on up to 11,421 BRCA1 and 7,080 BRCA2 carriers, of whom 4,310 had been affected with breast cancer and had information on either ER or PR status of the tumour, to assess the associations of 12 loci with breast cancer tumour characteristics. Associations were evaluated using a retrospective cohort approach. RESULTS: The results suggested stronger associations with ER-positive breast cancer than ER-negative for 11 loci in both BRCA1 and BRCA2 carriers. Among BRCA1 carriers, single nucleotide polymorphism (SNP) rs2981582 (FGFR2) exhibited the biggest difference based on ER status (per-allele hazard ratio (HR) for ER-positive = 1.35, 95% CI: 1.17 to 1.56 vs HR = 0.91, 95% CI: 0.85 to 0.98 for ER-negative, P-heterogeneity = 6.5 x 10-6). In contrast, SNP rs2046210 at 6q25.1 near ESR1 was primarily associated with ER-negative breast cancer risk for both BRCA1 and BRCA2 carriers. In BRCA2 carriers, SNPs in FGFR2, TOX3, LSP1, SLC4A7/NEK10, 5p12, 2q35, and 1p11.2 were significantly associated with ER-positive but not ER-negative disease. Similar results were observed when differentiating breast cancer cases by PR status. CONCLUSIONS: The associations of the 12 SNPs with risk for BRCA1 and BRCA2 carriers differ by ER-positive or ER-negative breast cancer status. The apparent differences in SNP associations between BRCA1 and BRCA2 carriers, and non-carriers, may be explicable by differences in the prevalence of tumour subtypes. As more risk modifying variants are identified, incorporating these associations into breast cancer subtype-specific

Published
2011

40. Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers

Author

Antoniou, A.C., Kartsonaki, C., Sinilnikova, O.M., Soucy, P., McGuffog, L., Healey, S., Lee, A., Peterlongo, P., Manoukian, S., Peissel, B., Zaffaroni, D., Cattaneo, E., Barile, M., Pensotti, V., Pasini, B., Dolcetti, R., Giannini, G., Putignano, A.L., Varesco, L., Radice, P., Mai, P.L., Greene, M.H., Andrulis, I.L., Glendon, G., Ozcelik, H., Thomassen, M., Gerdes, A.M., Kruse, T.A., Birk Jensen, U., Cruger, D.G., Caligo, M.A., Laitman, Y., Milgrom, R., Kaufman, B., Paluch-Shimon, S., Friedman, E., Loman, N., Harbst, K., Lindblom, A., Arver, B., Ehrencrona, H., Melin, B., Nathanson, K.L., Domchek, S.M., Rebbeck, T., Jakubowska, A., Lubinski, J., Gronwald, J., Huzarski, T., Byrski, T., Cybulski, C., Gorski, B., Osorio, A., Ramon Y Cajal, T., Fostira, F., Andres, R., Benitez, J., Hamann, U., Hogervorst, F.B.L., Rookus, M.A., Hooning, M.J., Nelen, M.R., Luijt, R.B. van der, Os, T.A. van, Asperen, C.J. van, Devilee, P., Meijers-Heijboer, H.E., Garcia, E.B., Peock, S., Cook, M., Frost, D., Platte, R., Leyland, J., Evans, D.G., Lalloo, F., Eeles, R., Izatt, L., Adlard, J., Davidson, R., Eccles, D., Ong, K.R., Cook, J., Douglas, F., Paterson, J., Kennedy, M.J., Miedzybrodzka, Z., Godwin, A., Stoppa-Lyonnet, D., Buecher, B., Belotti, M., Tirapo, C., Mazoyer, S., Barjhoux, L., Lasset, C., Leroux, D., Faivre, L., Bronner, M., Prieur, F., Nogues, C., Rouleau, E., et al., Antoniou, A.C., Kartsonaki, C., Sinilnikova, O.M., Soucy, P., McGuffog, L., Healey, S., Lee, A., Peterlongo, P., Manoukian, S., Peissel, B., Zaffaroni, D., Cattaneo, E., Barile, M., Pensotti, V., Pasini, B., Dolcetti, R., Giannini, G., Putignano, A.L., Varesco, L., Radice, P., Mai, P.L., Greene, M.H., Andrulis, I.L., Glendon, G., Ozcelik, H., Thomassen, M., Gerdes, A.M., Kruse, T.A., Birk Jensen, U., Cruger, D.G., Caligo, M.A., Laitman, Y., Milgrom, R., Kaufman, B., Paluch-Shimon, S., Friedman, E., Loman, N., Harbst, K., Lindblom, A., Arver, B., Ehrencrona, H., Melin, B., Nathanson, K.L., Domchek, S.M., Rebbeck, T., Jakubowska, A., Lubinski, J., Gronwald, J., Huzarski, T., Byrski, T., Cybulski, C., Gorski, B., Osorio, A., Ramon Y Cajal, T., Fostira, F., Andres, R., Benitez, J., Hamann, U., Hogervorst, F.B.L., Rookus, M.A., Hooning, M.J., Nelen, M.R., Luijt, R.B. van der, Os, T.A. van, Asperen, C.J. van, Devilee, P., Meijers-Heijboer, H.E., Garcia, E.B., Peock, S., Cook, M., Frost, D., Platte, R., Leyland, J., Evans, D.G., Lalloo, F., Eeles, R., Izatt, L., Adlard, J., Davidson, R., Eccles, D., Ong, K.R., Cook, J., Douglas, F., Paterson, J., Kennedy, M.J., Miedzybrodzka, Z., Godwin, A., Stoppa-Lyonnet, D., Buecher, B., Belotti, M., Tirapo, C., Mazoyer, S., Barjhoux, L., Lasset, C., Leroux, D., Faivre, L., Bronner, M., Prieur, F., Nogues, C., Rouleau, E., and et al.

Abstract

Item does not contain fulltext, Two single nucleotide polymorphisms (SNPs) at 6q25.1, near the ESR1 gene, have been implicated in the susceptibility to breast cancer for Asian (rs2046210) and European women (rs9397435). A genome-wide association study in Europeans identified two further breast cancer susceptibility variants: rs11249433 at 1p11.2 and rs999737 in RAD51L1 at 14q24.1. Although previously identified breast cancer susceptibility variants have been shown to be associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers, the involvement of these SNPs to breast cancer susceptibility in mutation carriers is currently unknown. To address this, we genotyped these SNPs in BRCA1 and BRCA2 mutation carriers from 42 studies from the Consortium of Investigators of Modifiers of BRCA1/2. In the analysis of 14 123 BRCA1 and 8053 BRCA2 mutation carriers of European ancestry, the 6q25.1 SNPs (r(2) = 0.14) were independently associated with the risk of breast cancer for BRCA1 mutation carriers [hazard ratio (HR) = 1.17, 95% confidence interval (CI): 1.11-1.23, P-trend = 4.5 x 10(-9) for rs2046210; HR = 1.28, 95% CI: 1.18-1.40, P-trend = 1.3 x 10(-8) for rs9397435], but only rs9397435 was associated with the risk for BRCA2 carriers (HR = 1.14, 95% CI: 1.01-1.28, P-trend = 0.031). SNP rs11249433 (1p11.2) was associated with the risk of breast cancer for BRCA2 mutation carriers (HR = 1.09, 95% CI: 1.02-1.17, P-trend = 0.015), but was not associated with breast cancer risk for BRCA1 mutation carriers (HR = 0.97, 95% CI: 0.92-1.02, P-trend = 0.20). SNP rs999737 (RAD51L1) was not associated with breast cancer risk for either BRCA1 or BRCA2 mutation carriers (P-trend = 0.27 and 0.30, respectively). The identification of SNPs at 6q25.1 associated with breast cancer risk for BRCA1 mutation carriers will lead to a better understanding of the biology of tumour development in these women.

Published
2011

41. Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers

Author

Antoniou, A.C. (Antonis), Kartsonaki, C. (Christiana), Sinilnikova, O. (Olga), Soucy, P. (Penny), McGuffog, L. (Lesley), Healey, S. (Sue), Lee, A. (Andrew), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Cattaneo, E. (Elisa), Barile, M. (Monica), Pensotti, V. (Valeria), Pasini, B. (Barbara), Dolcetti, R. (Riccardo), Giannini, G. (Giuseppe), Putignano, A.L., Varesco, L. (Liliana), Radice, P. (Paolo), Mai, P.L. (Phuong), Greene, M.H. (Mark), Andrulis, I.L. (Irene), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Thomassen, M. (Mads), Gerdes, A-M. (Anne-Marie), Kruse, T.A. (Torben), Jensen, U.B., Cruger, D. (Dorthe), Caligo, M.A. (Maria), Laitman, Y. (Yael), Milgrom, R. (Roni), Kaufman, B. (Bella), Paluch-Shimon, S. (Shani), Friedman, E. (Eitan), Loman, N. (Niklas), Harbst, K. (Katja), Lindblom, A. (Annika), Melin, B. (Beatrice), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Rebbeck, R. (Timothy), Jakubowska, A. (Anna), Lubinski, J. (Jan), Gronwald, J. (Jacek), Huzarski, T. (Tomasz), Byrski, T. (Tomasz), Cybulski, C. (Cezary), Górski, B. (Bohdan), Osorio, A. (Ana), Cajal, T.R., Fostira, F. (Florentia), Andres, R. (Raquel), Benitez, J. (Javier), Hamann, U. (Ute), Hogervorst, F.B.L. (Frans), Rookus, M.A. (Matti), Hooning, M.J. (Maartje), Nelen, M.R. (Marcel), Luijt, R.B. (Rob) van der, Os, T.A.M. (Theo) van, Asperen, C.J. (Christi) van, Devilee, P. (Peter), Meijers-Heijboer, H. (Hanne), Garcia, E.B.G., Peock, S. (Susan), Cook, M. (Margaret), Frost, D., Platte, R. (Radka), Leyland, J. (Jean), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Eeles, R. (Rosalind), Izatt, L. (Louise), Davidson, R. (Rosemarie), Eccles, D. (Diana), Ong, K.-R., Douglas, F. (Fiona), Paterson, J. (Joan), Kennedy, M.J. (John), Miedzybrodzka, Z. (Zosia), Godwin, A.K. (Andrew), Stoppa-Lyonnet, D. (Dominique), Buecher, B. (Bruno), Belotti, M. (Muriel), Tirapo, C. (Carole), Mazoyer, S. (Sylvie), Barjhoux, L. (Laure), Lasset, C. (Christine), Leroux, D. (Dominique), Faivre, L. (Laurence), Bronner, M. (Myriam), Prieur, F. (Fabienne), Nogues, C. (Catherine), Rouleau, E. (Etienne), Pujol, P. (Pascal), Coupier, I. (Isabelle), Frenay, M. (Marc), Hopper, J. (John), Daly, M.J. (Mark), Terry, M-B. (Mary-beth), John, E.M. (Esther), Buys, S.S. (Saundra), Yassin, Y. (Yosuf), Miron, A. (Alexander), Goldgar, D. (David), Singer, C.F. (Christian), Tea, M.-K., Pfeiler, G. (Georg), Dressler, C. (Catherina), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Ejlertsen, B. (Bent), Barkardottir, R.B. (Rosa), Kircchoff, T. (Tomas), Offit, K. (Kenneth), Piedmonte, M. (Marion), Rodriguez, G.C. (Gustavo), Small, L. (Laurie), Boggess, J.F. (John), Blank, S.V. (Stephanie), Basil, J. (Jack), Azodi, M. (Masoud), Toland, A.E. (Amanda), Montagna, M. (Marco), Tognazzo, S. (Silvia), Agata, S. (Simona), Imyanitov, E.N. (Evgeny), Janavicius, R. (Ramunas), Lázaro, C. (Conxi), Blanco, I. (Ignacio), Pharoah, P.D.P. (Paul), Sucheston, L. (Lara), Karlan, B.Y. (Beth), Walsh, C.S. (Christine), Olah, E. (Edith), Bozsik, A. (Aniko), Teo, S.-H. (Soo-Hwang), Seldon, J.L. (Joyce), Beattie, M.S. (Mary), Rensburg, E.J. (Elizabeth) van, Sluiter, M.D. (Michelle), Diez, O. (Orland), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Engel, C. (Christoph), Meindl, A. (Alfons), Ruehl, I. (Ina), Varon-Mateeva, R. (Raymonda), Kast, K. (Karin), Deissler, H. (Helmut), Niederacher, D. (Dieter), Arnold, N. (Norbert), Gadzicki, D. (Dorothea), Schönbuchner, I. (Ines), Caldes, T. (Trinidad), Hoya, M. (Miguel) de La, Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Dumont, M. (Martine), Chiquette, J. (Jocelyne), Tischkowitz, M. (Marc), Chenevix-Trench, G. (Georgia), Beesley, J. (Jonathan), Spurdle, A.B. (Amanda), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Fredericksen, Z. (Zachary), Wang, X. (Xing), Pankratz, V.S. (Shane), Couch, F.J. (Fergus), Simard, J. (Jacques), Easton, D.F. (Douglas), Karlsson, P. (Per), Nordling, M. (Margareta), Bergman, A. (Annika), Einbeigi, Z. (Zakaria), Stenmark-Askmalm, M. (M.), Liedgren, S. (Sigrun), Borg, Å. (Åke), Olsson, H. (Hans), Kristoffersson, U. (Ulf), Jernström, H. (H.), Henriksson, K. (Karin), Wachenfeldt, A. (Anna) von, Liljegren, A. (Annelie), Barbany-Bustinza, G. (Gisela), Rantala, J. (Johanna), Grönberg, H. (Henrik), Stattin, E.-L., Emanuelsson, M. (Monica), Brandell, R.R., Dahl, N. (Niklas), Verhoef, S., Verheus, M. (Martijn), Veer, L.J. (Laura) van 't, Leeuwen, F.E. (Flora) van, Collée, J.M. (Margriet), Ouweland, A.M.W. (Ans) van den, Jager, A. (Agnes), Tilanus-Linthorst, M.M.A. (Madeleine), Seynaeve, C.M. (Caroline), Wijnen, J.T. (Juul), Vreeswijk, M.P. (Maaike), Tollenaar, R.A.E.M. (Rob), Ligtenberg, M.J. (Marjolijn), Hoogerbrugge, N. (Nicoline), Ausems, M.G.E.M. (Margreet), Aalfs, C.M. (Cora), Gille, J.J.P. (Jan), Waisfisz, Q. (Quinten), Gómez García, E.B. (Encarna), Roozendaal, C.E. (Cees) van, Blok, M.J. (Marinus), Caanen, B., Oosterwijk, J.C., Hout, A.H. (Annemarie) van der, Mourits, M.J., Vasen, H.F. (Hans), Gregory, H. (Helen), Morrison, P.J. (Patrick), Jeffers, L. (Lisa), Cole, T.J. (Trevor), McKeown, C. (Carole), Hoffman, J. (Jonathan), Donaldson, A. (Alan), Downing, S. (Sarah), Taylor, A. (Amy), Murray, A. (Alexandra), Rogers, M.T. (Mark), McCann, E. (Emma), Porteous, M.E. (Mary), Drummond, S. (Sarah), Brewer, C. (Carole), Kivuva, E. (Emma), Searle, A. (Anne), Goodman, S. (Selina), Hill, K. (Kathryn), Murday, V. (Victoria), Bradshaw, N. (Nicola), Snadden, L. (Lesley), Longmuir, M. (Mark), Watt, C. (Catherine), Gibson, S. (Sarah), Haque, E. (Eshika), Tobias, E. (Ed), Duncan, A. (Alexis), Jacobs, C. (Chris), Langman, C. (Caroline), Whaite, A. (Anna), Dorkins, H. (Huw), Barwell, J. (Julian), Chu, C. (Chengbin), Miller, J. (Julie), Ellis, I.O. (Ian), Houghton, C. (Catherine), Side, L. (Lucy), Male, A. (Alison), Berlin, C. (Cheryl), Eason, J. (Jacqueline), Collier, R. (Rebecca), Claber, O. (Oonagh), Jobson, I. (Irene), Walker, L.J. (Lisa), McLeod, D. (Diane), Halliday, D. (Dorothy), Durell, S. (Sarah), Stayner, B. (Barbara), Shanley, S. (Susan), Rahman, N. (Nazneen), Houlston, R. (Richard), Bancroft, E.K. (Elizabeth), D'Mello, L. (Lucia), Page, E. (Elizabeth), Ardern-Jones, A. (Audrey), Kohut, K. (Kelly), Wiggins, J. (Jennifer), Castro, E. (Elena), Mitra, A. (Anita), Robertson, L. (Lisa), Quarrell, O. (Oliver), Bardsley, C. (Cathryn), Ehrencrona, H. (Hans), Hodgson, S.V. (Shirley), Barton, D.E. (David), Goff, S. (Sheila), Brice, G. (Glen), Winchester, L. (Lizzie), Eddy, C. (Charlotte), Tripathi, V. (Vishakha), Attard, V. (Virginia), Lucassen, A. (Anneke), Crawford, G. (Gillian), McBride, D. (Donna), Smalley, S. (Sarah), Adlard, J.W. (Julian), Arver, B. (Brita Wasteson), Antoniou, A.C. (Antonis), Kartsonaki, C. (Christiana), Sinilnikova, O. (Olga), Soucy, P. (Penny), McGuffog, L. (Lesley), Healey, S. (Sue), Lee, A. (Andrew), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Cattaneo, E. (Elisa), Barile, M. (Monica), Pensotti, V. (Valeria), Pasini, B. (Barbara), Dolcetti, R. (Riccardo), Giannini, G. (Giuseppe), Putignano, A.L., Varesco, L. (Liliana), Radice, P. (Paolo), Mai, P.L. (Phuong), Greene, M.H. (Mark), Andrulis, I.L. (Irene), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Thomassen, M. (Mads), Gerdes, A-M. (Anne-Marie), Kruse, T.A. (Torben), Jensen, U.B., Cruger, D. (Dorthe), Caligo, M.A. (Maria), Laitman, Y. (Yael), Milgrom, R. (Roni), Kaufman, B. (Bella), Paluch-Shimon, S. (Shani), Friedman, E. (Eitan), Loman, N. (Niklas), Harbst, K. (Katja), Lindblom, A. (Annika), Melin, B. (Beatrice), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Rebbeck, R. (Timothy), Jakubowska, A. (Anna), Lubinski, J. (Jan), Gronwald, J. (Jacek), Huzarski, T. (Tomasz), Byrski, T. (Tomasz), Cybulski, C. (Cezary), Górski, B. (Bohdan), Osorio, A. (Ana), Cajal, T.R., Fostira, F. (Florentia), Andres, R. (Raquel), Benitez, J. (Javier), Hamann, U. (Ute), Hogervorst, F.B.L. (Frans), Rookus, M.A. (Matti), Hooning, M.J. (Maartje), Nelen, M.R. (Marcel), Luijt, R.B. (Rob) van der, Os, T.A.M. (Theo) van, Asperen, C.J. (Christi) van, Devilee, P. (Peter), Meijers-Heijboer, H. (Hanne), Garcia, E.B.G., Peock, S. (Susan), Cook, M. (Margaret), Frost, D., Platte, R. (Radka), Leyland, J. (Jean), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Eeles, R. (Rosalind), Izatt, L. (Louise), Davidson, R. (Rosemarie), Eccles, D. (Diana), Ong, K.-R., Douglas, F. (Fiona), Paterson, J. (Joan), Kennedy, M.J. (John), Miedzybrodzka, Z. (Zosia), Godwin, A.K. (Andrew), Stoppa-Lyonnet, D. (Dominique), Buecher, B. (Bruno), Belotti, M. (Muriel), Tirapo, C. (Carole), Mazoyer, S. (Sylvie), Barjhoux, L. (Laure), Lasset, C. (Christine), Leroux, D. (Dominique), Faivre, L. (Laurence), Bronner, M. (Myriam), Prieur, F. (Fabienne), Nogues, C. (Catherine), Rouleau, E. (Etienne), Pujol, P. (Pascal), Coupier, I. (Isabelle), Frenay, M. (Marc), Hopper, J. (John), Daly, M.J. (Mark), Terry, M-B. (Mary-beth), John, E.M. (Esther), Buys, S.S. (Saundra), Yassin, Y. (Yosuf), Miron, A. (Alexander), Goldgar, D. (David), Singer, C.F. (Christian), Tea, M.-K., Pfeiler, G. (Georg), Dressler, C. (Catherina), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Ejlertsen, B. (Bent), Barkardottir, R.B. (Rosa), Kircchoff, T. (Tomas), Offit, K. (Kenneth), Piedmonte, M. (Marion), Rodriguez, G.C. (Gustavo), Small, L. (Laurie), Boggess, J.F. (John), Blank, S.V. (Stephanie), Basil, J. (Jack), Azodi, M. (Masoud), Toland, A.E. (Amanda), Montagna, M. (Marco), Tognazzo, S. (Silvia), Agata, S. (Simona), Imyanitov, E.N. (Evgeny), Janavicius, R. (Ramunas), Lázaro, C. (Conxi), Blanco, I. (Ignacio), Pharoah, P.D.P. (Paul), Sucheston, L. (Lara), Karlan, B.Y. (Beth), Walsh, C.S. (Christine), Olah, E. (Edith), Bozsik, A. (Aniko), Teo, S.-H. (Soo-Hwang), Seldon, J.L. (Joyce), Beattie, M.S. (Mary), Rensburg, E.J. (Elizabeth) van, Sluiter, M.D. (Michelle), Diez, O. (Orland), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Engel, C. (Christoph), Meindl, A. (Alfons), Ruehl, I. (Ina), Varon-Mateeva, R. (Raymonda), Kast, K. (Karin), Deissler, H. (Helmut), Niederacher, D. (Dieter), Arnold, N. (Norbert), Gadzicki, D. (Dorothea), Schönbuchner, I. (Ines), Caldes, T. (Trinidad), Hoya, M. (Miguel) de La, Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Dumont, M. (Martine), Chiquette, J. (Jocelyne), Tischkowitz, M. (Marc), Chenevix-Trench, G. (Georgia), Beesley, J. (Jonathan), Spurdle, A.B. (Amanda), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Fredericksen, Z. (Zachary), Wang, X. (Xing), Pankratz, V.S. (Shane), Couch, F.J. (Fergus), Simard, J. (Jacques), Easton, D.F. (Douglas), Karlsson, P. (Per), Nordling, M. (Margareta), Bergman, A. (Annika), Einbeigi, Z. (Zakaria), Stenmark-Askmalm, M. (M.), Liedgren, S. (Sigrun), Borg, Å. (Åke), Olsson, H. (Hans), Kristoffersson, U. (Ulf), Jernström, H. (H.), Henriksson, K. (Karin), Wachenfeldt, A. (Anna) von, Liljegren, A. (Annelie), Barbany-Bustinza, G. (Gisela), Rantala, J. (Johanna), Grönberg, H. (Henrik), Stattin, E.-L., Emanuelsson, M. (Monica), Brandell, R.R., Dahl, N. (Niklas), Verhoef, S., Verheus, M. (Martijn), Veer, L.J. (Laura) van 't, Leeuwen, F.E. (Flora) van, Collée, J.M. (Margriet), Ouweland, A.M.W. (Ans) van den, Jager, A. (Agnes), Tilanus-Linthorst, M.M.A. (Madeleine), Seynaeve, C.M. (Caroline), Wijnen, J.T. (Juul), Vreeswijk, M.P. (Maaike), Tollenaar, R.A.E.M. (Rob), Ligtenberg, M.J. (Marjolijn), Hoogerbrugge, N. (Nicoline), Ausems, M.G.E.M. (Margreet), Aalfs, C.M. (Cora), Gille, J.J.P. (Jan), Waisfisz, Q. (Quinten), Gómez García, E.B. (Encarna), Roozendaal, C.E. (Cees) van, Blok, M.J. (Marinus), Caanen, B., Oosterwijk, J.C., Hout, A.H. (Annemarie) van der, Mourits, M.J., Vasen, H.F. (Hans), Gregory, H. (Helen), Morrison, P.J. (Patrick), Jeffers, L. (Lisa), Cole, T.J. (Trevor), McKeown, C. (Carole), Hoffman, J. (Jonathan), Donaldson, A. (Alan), Downing, S. (Sarah), Taylor, A. (Amy), Murray, A. (Alexandra), Rogers, M.T. (Mark), McCann, E. (Emma), Porteous, M.E. (Mary), Drummond, S. (Sarah), Brewer, C. (Carole), Kivuva, E. (Emma), Searle, A. (Anne), Goodman, S. (Selina), Hill, K. (Kathryn), Murday, V. (Victoria), Bradshaw, N. (Nicola), Snadden, L. (Lesley), Longmuir, M. (Mark), Watt, C. (Catherine), Gibson, S. (Sarah), Haque, E. (Eshika), Tobias, E. (Ed), Duncan, A. (Alexis), Jacobs, C. (Chris), Langman, C. (Caroline), Whaite, A. (Anna), Dorkins, H. (Huw), Barwell, J. (Julian), Chu, C. (Chengbin), Miller, J. (Julie), Ellis, I.O. (Ian), Houghton, C. (Catherine), Side, L. (Lucy), Male, A. (Alison), Berlin, C. (Cheryl), Eason, J. (Jacqueline), Collier, R. (Rebecca), Claber, O. (Oonagh), Jobson, I. (Irene), Walker, L.J. (Lisa), McLeod, D. (Diane), Halliday, D. (Dorothy), Durell, S. (Sarah), Stayner, B. (Barbara), Shanley, S. (Susan), Rahman, N. (Nazneen), Houlston, R. (Richard), Bancroft, E.K. (Elizabeth), D'Mello, L. (Lucia), Page, E. (Elizabeth), Ardern-Jones, A. (Audrey), Kohut, K. (Kelly), Wiggins, J. (Jennifer), Castro, E. (Elena), Mitra, A. (Anita), Robertson, L. (Lisa), Quarrell, O. (Oliver), Bardsley, C. (Cathryn), Ehrencrona, H. (Hans), Hodgson, S.V. (Shirley), Barton, D.E. (David), Goff, S. (Sheila), Brice, G. (Glen), Winchester, L. (Lizzie), Eddy, C. (Charlotte), Tripathi, V. (Vishakha), Attard, V. (Virginia), Lucassen, A. (Anneke), Crawford, G. (Gillian), McBride, D. (Donna), Smalley, S. (Sarah), Adlard, J.W. (Julian), and Arver, B. (Brita Wasteson)

Abstract

Two single nucleotide polymorphisms (SNPs) at 6q25.1, near the ESR1 gene, have been implicated in the susceptibility to breast cancer for Asian (rs2046210) and European women (rs9397435). A genome-wide association study in Europeans identified two further breast cancer susceptibility variants: rs11249433 at 1p11.2 and rs999737 in RAD51L1 at 14q24.1. Although previously identified breast cancer susceptibility variants have been shown to be associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers, the involvement of these SNPs to breast cancer susceptibility in mutation carriers is currently unknown. To address this, we genotyped these SNPs in BRCA1 and BRCA2 mutation carriers from 42 studies from the Consortium of Investigators of Modifiers of BRCA1/2. In the analysis of 14 123 BRCA1 and 8053 BRCA2 mutation carriers of European ancestry, the 6q25.1 SNPs (r2= 0.14) were independently associated with the risk of breast cancer for BRCA1 mutation carriers [hazard ratio (HR) = 1.17, 95% confidence interval (CI): 1.11-1.23, P-trend = 4.5 × 10-9for rs2046210; HR = 1.28, 95% CI: 1.18-1.40, P-trend = 1.3 × 10-8for rs9397435], but only rs9397435 was associated with the risk for BRCA2 carriers (HR = 1.14, 95% CI: 1.01-1.28, P-trend = 0.031). SNP rs11249433 (1p11.2) was associated with the risk of breast cancer for BRCA2 mutation carriers (HR = 1.09, 95% CI: 1.02-1.17, P-trend = 0.015), but was not associated with breast cancer risk for BRCA1 mutation carriers (HR = 0.97, 95% CI: 0.92-1.02, P-trend = 0.20). SNP rs999737 (RAD51L1) was not associated with breast cancer risk for either BRCA1 or BRCA2 mutation carriers (P-trend = 0.27 and 0.30, respectively). The identification of SNPs at 6q25.1 associated with breast cancer risk for BRCA1 mutation carriers will lead to a better understanding of the biology of tumour development in these women.

Published
2011
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42. Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2

Author

Mulligan, A.M. (Anna Marie), Couch, F.J. (Fergus), Barrowdale, D. (Daniel), Domchek, S.M. (Susan), Eccles, D. (Diana), Nevanlinna, H. (Heli), Ramus, S.J. (Susan), Robson, M. (Mark), Sherman, M.E. (Mark), Spurdle, A.B. (Amanda), Wapenschmidt, B. (Barbara), Lee, A. (Andrew), McGuffog, L. (Lesley), Healey, S. (Sue), Sinilnikova, O. (Olga), Janavicius, R. (Ramunas), Hansen, T.V.O. (Thomas), Nielsen, F.C. (Finn), Ejlertsen, B. (Bent), Osorio, A. (Ana), Muñoz-Repeto, I. (Iván), Durán, M. (Mercedes), Godino, J. (Javier), Pertesi, M. (Maroulio), Benítez, J. (Javier), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Cattaneo, E. (Elisa), Bonnani, B. (Bernardo), Viel, A. (Alessandra), Pasini, B. (Barbara), Papi, L. (Laura), Ottini, L. (Laura), Savarese, A. (Antonella), Bernard, L. (Loris), Radice, P. (Paolo), Hamann, U. (Ute), Verheus, M. (Martijn), Meijers-Heijboer, E.J. (Hanne), Wijnen, J.T. (Juul), Gómez García, E.B. (Encarna), Nelen, M.R. (Marcel), Kets, C.M. (Marleen), Seynaeve, C.M. (Caroline), Tilanus-Linthorst, M.M.A. (Madeleine), Luijt, R.B. (Rob) van der, Os, T.V. (Theo), Rookus, M.A. (Matti), Frost, D. (Debra), Jones, J.L. (J Louise), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Eeles, R. (Rosalind), Izatt, L. (Louise), Adlard, J.W. (Julian), Davidson, R. (Rosemarie), Cook, J. (Jackie), Donaldson, A. (Alan), Dorkins, H. (Huw), Gregory, H. (Helen), Eason, J. (Jacqueline), Houghton, C. (Catherine), Barwell, J. (Julian), Side, L. (Lucy), McCann, E. (Emma), Murray, A. (Alexandra), Peock, S. (Susan), Godwin, A.K. (Andrew), Schmutzler, R.K. (Rita), Rhiem, K. (Kerstin), Engel, C. (Christoph), Meindl, A. (Alfons), Ruehl, I. (Ina), Arnold, N. (Norbert), Niederacher, D. (Dieter), Sutter, C. (Christian), Deissler, H. (Helmut), Gadzicki, D. (Dorothea), Kast, K. (Karin), Preisler-Adams, S. (Sabine), Varon-Mateeva, R. (Raymonda), Schoenbuchner, I. (Ines), Fiebig, B. (Britta), Heinritz, W. (Wolfram), Schäfer, D. (Dieter), Gevensleben, H. (Heidrun), Caux-Moncoutier, V. (Virginie), Fassy-Colcombet, M. (Marion), Cornelis, F. (Franco̧is), Mazoyer, S. (Sylvie), Léone, M. (Mélanie), Boutry-Kryza, N. (N.), Hardouin, A. (Agnès), Berthet, P. (Pascaline), Muller, D.W. (Danièle), Fricker, J.P. (Jean Pierre), Mortemousque, I. (Isabelle), Pujol, P. (Pascal), Coupier, I. (Isabelle), Lebrun, M. (Marine), Kientz, C. (Caroline), Longy, M. (Michel), Sevenet, N. (Nicolas), Stoppa-Lyonnet, D. (Dominique), Isaacs, C. (Claudine), Caldes, T. (Trinidad), Hoya, M. (Miguel) de La, Heikinen, T. (Tuomas), Aittomäki, K. (Kristiina), Blanco, I. (Ignacio), Lázaro, C. (Conxi), Barkardottir, R.B. (Rosa), Soucy, P. (Penny), Dumont, M. (Martine), Simard, J. (Jacques), Montagna, M. (Marco), Tognazzo, S. (Silvia), D'Andrea, E. (Emma), Fox, S.B. (Stephen), Yan, M. (Max), Rebbeck, R. (Timothy), Olopade, O.I. (Olofunmilayo), Weitzel, J.N. (Jeffrey), Lynch, H. (Henry), Ganz, P.A. (Patricia), Tomlinson, G. (Gail), Wang, X. (Xing), Fredericksen, Z. (Zachary), Pankratz, V.S. (Shane), Lindor, N.M. (Noralane), Szabo, C. (Csilla), Offit, K. (Kenneth), Sakr, R. (Rita), Gaudet, M.M. (Mia), Bhatia, K.P. (Kailash), Kauff, N. (Noah), Singer, C.F. (Christian), Tea, M.-K., Gschwantler-Kaulich, D. (Daphne), Fink-Retter, A. (Anneliese), Mai, P.L. (Phuong), Greene, M.H. (Mark), Imyanitov, E.N. (Evgeny), O'Malley, F.P. (Frances), Ozcelik, H. (Hilmi), Glendon, G. (Gord), Toland, A.E. (Amanda), Gerdes, A-M. (Anne-Marie), Thomassen, M. (Mads), Kruse, T.A. (Torben), Jensen, U.B., Skytte, A.-B. (Anne-Bine), Caligo, M.A. (Maria), Soller, M. (Maria), Henriksson, K. (Karin), Wachenfeldt, A. (Anna) von, Arver, B. (Brita Wasteson), Stenmark-Askmalm, M. (M.), Karlsson, P. (Per), Ding, Y.C. (Yuan), Neuhausen, S.L. (Susan), Beattie, M.S. (Mary), Pharoah, P.D.P. (Paul), Moysich, K.B. (Kirsten), Nathanson, K.L. (Katherine), Karlan, B.Y. (Beth), Gross, J. (Jenny), John, E.M. (Esther), Daly, M.B. (Mary), Buys, S.S. (Saundra), Southey, M.C. (Melissa), Hopper, J.L. (John), Terry, M.-B. (Mary-Beth), Chung, W. (Wendy), Miron, A. (Alexander), Goldgar, D. (David), Chenevix-Trench, G. (Georgia), Easton, D.F. (Douglas), Andrulis, I.L. (Irene), Antoniou, A.C. (Antonis), Mulligan, A.M. (Anna Marie), Couch, F.J. (Fergus), Barrowdale, D. (Daniel), Domchek, S.M. (Susan), Eccles, D. (Diana), Nevanlinna, H. (Heli), Ramus, S.J. (Susan), Robson, M. (Mark), Sherman, M.E. (Mark), Spurdle, A.B. (Amanda), Wapenschmidt, B. (Barbara), Lee, A. (Andrew), McGuffog, L. (Lesley), Healey, S. (Sue), Sinilnikova, O. (Olga), Janavicius, R. (Ramunas), Hansen, T.V.O. (Thomas), Nielsen, F.C. (Finn), Ejlertsen, B. (Bent), Osorio, A. (Ana), Muñoz-Repeto, I. (Iván), Durán, M. (Mercedes), Godino, J. (Javier), Pertesi, M. (Maroulio), Benítez, J. (Javier), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Cattaneo, E. (Elisa), Bonnani, B. (Bernardo), Viel, A. (Alessandra), Pasini, B. (Barbara), Papi, L. (Laura), Ottini, L. (Laura), Savarese, A. (Antonella), Bernard, L. (Loris), Radice, P. (Paolo), Hamann, U. (Ute), Verheus, M. (Martijn), Meijers-Heijboer, E.J. (Hanne), Wijnen, J.T. (Juul), Gómez García, E.B. (Encarna), Nelen, M.R. (Marcel), Kets, C.M. (Marleen), Seynaeve, C.M. (Caroline), Tilanus-Linthorst, M.M.A. (Madeleine), Luijt, R.B. (Rob) van der, Os, T.V. (Theo), Rookus, M.A. (Matti), Frost, D. (Debra), Jones, J.L. (J Louise), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Eeles, R. (Rosalind), Izatt, L. (Louise), Adlard, J.W. (Julian), Davidson, R. (Rosemarie), Cook, J. (Jackie), Donaldson, A. (Alan), Dorkins, H. (Huw), Gregory, H. (Helen), Eason, J. (Jacqueline), Houghton, C. (Catherine), Barwell, J. (Julian), Side, L. (Lucy), McCann, E. (Emma), Murray, A. (Alexandra), Peock, S. (Susan), Godwin, A.K. (Andrew), Schmutzler, R.K. (Rita), Rhiem, K. (Kerstin), Engel, C. (Christoph), Meindl, A. (Alfons), Ruehl, I. (Ina), Arnold, N. (Norbert), Niederacher, D. (Dieter), Sutter, C. (Christian), Deissler, H. (Helmut), Gadzicki, D. (Dorothea), Kast, K. (Karin), Preisler-Adams, S. (Sabine), Varon-Mateeva, R. (Raymonda), Schoenbuchner, I. (Ines), Fiebig, B. (Britta), Heinritz, W. (Wolfram), Schäfer, D. (Dieter), Gevensleben, H. (Heidrun), Caux-Moncoutier, V. (Virginie), Fassy-Colcombet, M. (Marion), Cornelis, F. (Franco̧is), Mazoyer, S. (Sylvie), Léone, M. (Mélanie), Boutry-Kryza, N. (N.), Hardouin, A. (Agnès), Berthet, P. (Pascaline), Muller, D.W. (Danièle), Fricker, J.P. (Jean Pierre), Mortemousque, I. (Isabelle), Pujol, P. (Pascal), Coupier, I. (Isabelle), Lebrun, M. (Marine), Kientz, C. (Caroline), Longy, M. (Michel), Sevenet, N. (Nicolas), Stoppa-Lyonnet, D. (Dominique), Isaacs, C. (Claudine), Caldes, T. (Trinidad), Hoya, M. (Miguel) de La, Heikinen, T. (Tuomas), Aittomäki, K. (Kristiina), Blanco, I. (Ignacio), Lázaro, C. (Conxi), Barkardottir, R.B. (Rosa), Soucy, P. (Penny), Dumont, M. (Martine), Simard, J. (Jacques), Montagna, M. (Marco), Tognazzo, S. (Silvia), D'Andrea, E. (Emma), Fox, S.B. (Stephen), Yan, M. (Max), Rebbeck, R. (Timothy), Olopade, O.I. (Olofunmilayo), Weitzel, J.N. (Jeffrey), Lynch, H. (Henry), Ganz, P.A. (Patricia), Tomlinson, G. (Gail), Wang, X. (Xing), Fredericksen, Z. (Zachary), Pankratz, V.S. (Shane), Lindor, N.M. (Noralane), Szabo, C. (Csilla), Offit, K. (Kenneth), Sakr, R. (Rita), Gaudet, M.M. (Mia), Bhatia, K.P. (Kailash), Kauff, N. (Noah), Singer, C.F. (Christian), Tea, M.-K., Gschwantler-Kaulich, D. (Daphne), Fink-Retter, A. (Anneliese), Mai, P.L. (Phuong), Greene, M.H. (Mark), Imyanitov, E.N. (Evgeny), O'Malley, F.P. (Frances), Ozcelik, H. (Hilmi), Glendon, G. (Gord), Toland, A.E. (Amanda), Gerdes, A-M. (Anne-Marie), Thomassen, M. (Mads), Kruse, T.A. (Torben), Jensen, U.B., Skytte, A.-B. (Anne-Bine), Caligo, M.A. (Maria), Soller, M. (Maria), Henriksson, K. (Karin), Wachenfeldt, A. (Anna) von, Arver, B. (Brita Wasteson), Stenmark-Askmalm, M. (M.), Karlsson, P. (Per), Ding, Y.C. (Yuan), Neuhausen, S.L. (Susan), Beattie, M.S. (Mary), Pharoah, P.D.P. (Paul), Moysich, K.B. (Kirsten), Nathanson, K.L. (Katherine), Karlan, B.Y. (Beth), Gross, J. (Jenny), John, E.M. (Esther), Daly, M.B. (Mary), Buys, S.S. (Saundra), Southey, M.C. (Melissa), Hopper, J.L. (John), Terry, M.-B. (Mary-Beth), Chung, W. (Wendy), Miron, A. (Alexander), Goldgar, D. (David), Chenevix-Trench, G. (Georgia), Easton, D.F. (Douglas), Andrulis, I.L. (Irene), and Antoniou, A.C. (Antonis)

Abstract

Introduction: Previous studies have demonstrated that common breast cancer susceptibility alleles are differentially associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. It is currently unknown how these alleles are associated with different breast cancer subtypes in BRCA1 and BRCA2 mutation carriers defined by estrogen (ER) or progesterone receptor (PR) status of the tumour.Methods: We used genotype data on up to 11,421 BRCA1 and 7,080 BRCA2 carriers, of whom 4,310 had been affected with breast cancer and had information on either ER or PR status of the tumour, to assess the associations of 12 loci with breast cancer tumour characteristics. Associations were evaluated using a retrospective cohort approach.Results: The results suggested stronger associations with ER-positive breast cancer than ER-negative for 11 loci in both BRCA1 and BRCA2 carriers. Among BRCA1 carriers, single nucleotide polymorphism (SNP) rs2981582 (FGFR2) exhibited the biggest difference based on ER status (per-allele hazard ratio (HR) for ER-positive = 1.35, 95% CI: 1.17 to 1.56 vs HR = 0.91, 95% CI: 0.85 to 0.98 for ER-negative, P-heterogeneity = 6.5 × 10-6). In contrast, SNP rs2046210 at 6q25.1 near ESR1 was primarily associated with ER-negative breast cancer risk for both BRCA1 and BRCA2 carriers. In BRCA2 carriers, SNPs in FGFR2, TOX3, LSP1, SLC4A7/NEK10, 5p12, 2q35, and 1p11.2 were significantly associated with ER-positive but not ER-negative disease. Similar results were observed when differentiating breast cancer cases by PR status.Conclusions: The associations of the 12 SNPs with risk for BRCA1 and BRCA2 carriers differ by ER-positive or ER-negative breast cancer status. The apparent differences in SNP associations between BRCA1 and BRCA2 carriers, and non-carriers, may be explicable by differences in the prevalence of tumour subtypes. As more risk modifying variants are identified, incorporating these associations into breast cancer subtype-specific risk models

Published
2011
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43. A co-segregating microduplication of chromosome 15q11.2 pinpoints two risk genes for autism spectrum disorder

Author

Zwaag, B. (Bert) van der, Staal, W.G. (Wouter), Hochstenbach, R. (Ron), Poot, M. (Martin), Spierenburg, H.A. (Henk), Jonge, M.V. (Maretha) de, Verbeek, N.E. (Nienke), Slot, R. (Ruben) van 't, Es, M.A. (Michael) van, Freitag, C.M. (Christine), Buizer-Voskamp, J.E. (Jacobine), Nelen, M.R. (Marcel), Berg, L.H. (Leonard) van den, Ploos van Amstel, H.K. (Hans), Engeland, H. (Herman) van, Burbach, J.P.H. (Peter), Zwaag, B. (Bert) van der, Staal, W.G. (Wouter), Hochstenbach, R. (Ron), Poot, M. (Martin), Spierenburg, H.A. (Henk), Jonge, M.V. (Maretha) de, Verbeek, N.E. (Nienke), Slot, R. (Ruben) van 't, Es, M.A. (Michael) van, Freitag, C.M. (Christine), Buizer-Voskamp, J.E. (Jacobine), Nelen, M.R. (Marcel), Berg, L.H. (Leonard) van den, Ploos van Amstel, H.K. (Hans), Engeland, H. (Herman) van, and Burbach, J.P.H. (Peter)

Abstract

High resolution genomic copy-number analysis has shown that inherited and de novo copy-number variations contribute significantly to autism pathology, and that identification of small chromosomal aberrations related to autism will expedite the discovery of risk genes involved. Here, we report a microduplication of chromosome 15q11.2, spanning only four genes, co-segregating with autism in a Dutch pedigree, identified by SNP microarray analysis, and independently confirmed by FISH and MLPA analysis. Quantitative RT-PCR analysis revealed over 70% increase in peripheral blood mRNA levels for the four genes present in the duplicated region in patients, and RNA in situ hybridization on mouse embryonic and adult brain sections revealed that two of the four genes, CYFIP1 and NIPA1, were highly expressed in the developing mouse brain. These findings point towards a contribution of microduplications at chromosome 15q11.2 to autism, and highlight CYFIP1 and NIPA1 as autism risk genes functioning in axonogenesis and synaptogenesis. Thereby, these findings further implicate defects in dosage-sensitive molecular control of neuronal connectivity in autism. However, the prevalence of this microduplication in patient samples was statistically not significantly different from control samples (0.94%in patients vs. 0.42%controls, P=0.247), which suggests that our findings should be interpreted with caution and indicates the need for studies that include large numbers of control subjects to ascertain the impact of these changes on a population scale.

Published
2010
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44. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes.

Author

Mefford, H.C., Sharp, A.J., Baker, C., Itsara, A., Jiang, Z., Buysse, K., Huang, S., Maloney, V.K., Crolla, J.A., Baralle, D., Collins, A., Mercer, C., Norga, K., Ravel, T. de, Devriendt, K., Bongers, E.M.H.F., Leeuw, N. de, Reardon, W., Gimelli, S., Bena, F., Hennekam, R.C.M., Male, A., Gaunt, L., Clayton-Smith, J., Simonic, I., Park, S.M., Mehta, S.G., Nik-Zainal, S., Woods, C.G., Firth, H.V., Parkin, G., Fichera, M., Reitano, S., Giudice, M. Lo, Li, K.E., Casuga, I., Broomer, A., Conrad, B., Schwerzmann, M., Raber, L., Gallati, S., Striano, P., Coppola, A., Tolmie, J.L., Tobias, E.S., Lilley, C., Armengol, L., Spysschaert, Y., Verloo, P., Coene, A. De, Goossens, L., Mortier, G., Speleman, F., Binsbergen, E. van, Nelen, M.R., Hochstenbach, R., Poot, M., Gallagher, L., Gill, M., McClellan, J., King, M.C., Regan, R., Skinner, C., Stevenson, R.E., Antonarakis, S.E., Chen, C., Estivill, X., Menten, B., Gimelli, G., Gribble, S.M., Schwartz, S., Sutcliffe, J.S., Walsh, T., Knight, S.J., Sebat, J., Romano, C, Schwartz, C.E., Veltman, J.A., Vries, L.B.A. de, Vermeesch, J.R., Barber, J.C., Willatt, L., Tassabehji, M., Eichler, E.E., Mefford, H.C., Sharp, A.J., Baker, C., Itsara, A., Jiang, Z., Buysse, K., Huang, S., Maloney, V.K., Crolla, J.A., Baralle, D., Collins, A., Mercer, C., Norga, K., Ravel, T. de, Devriendt, K., Bongers, E.M.H.F., Leeuw, N. de, Reardon, W., Gimelli, S., Bena, F., Hennekam, R.C.M., Male, A., Gaunt, L., Clayton-Smith, J., Simonic, I., Park, S.M., Mehta, S.G., Nik-Zainal, S., Woods, C.G., Firth, H.V., Parkin, G., Fichera, M., Reitano, S., Giudice, M. Lo, Li, K.E., Casuga, I., Broomer, A., Conrad, B., Schwerzmann, M., Raber, L., Gallati, S., Striano, P., Coppola, A., Tolmie, J.L., Tobias, E.S., Lilley, C., Armengol, L., Spysschaert, Y., Verloo, P., Coene, A. De, Goossens, L., Mortier, G., Speleman, F., Binsbergen, E. van, Nelen, M.R., Hochstenbach, R., Poot, M., Gallagher, L., Gill, M., McClellan, J., King, M.C., Regan, R., Skinner, C., Stevenson, R.E., Antonarakis, S.E., Chen, C., Estivill, X., Menten, B., Gimelli, G., Gribble, S.M., Schwartz, S., Sutcliffe, J.S., Walsh, T., Knight, S.J., Sebat, J., Romano, C, Schwartz, C.E., Veltman, J.A., Vries, L.B.A. de, Vermeesch, J.R., Barber, J.C., Willatt, L., Tassabehji, M., and Eichler, E.E.

Abstract

Contains fulltext : 71235.pdf (publisher's version ) (Open Access), BACKGROUND: Duplications and deletions in the human genome can cause disease or predispose persons to disease. Advances in technologies to detect these changes allow for the routine identification of submicroscopic imbalances in large numbers of patients. METHODS: We tested for the presence of microdeletions and microduplications at a specific region of chromosome 1q21.1 in two groups of patients with unexplained mental retardation, autism, or congenital anomalies and in unaffected persons. RESULTS: We identified 25 persons with a recurrent 1.35-Mb deletion within 1q21.1 from screening 5218 patients. The microdeletions had arisen de novo in eight patients, were inherited from a mildly affected parent in three patients, were inherited from an apparently unaffected parent in six patients, and were of unknown inheritance in eight patients. The deletion was absent in a series of 4737 control persons (P=1.1x10(-7)). We found considerable variability in the level of phenotypic expression of the microdeletion; phenotypes included mild-to-moderate mental retardation, microcephaly, cardiac abnormalities, and cataracts. The reciprocal duplication was enriched in nine children with mental retardation or autism spectrum disorder and other variable features (P=0.02). We identified three deletions and three duplications of the 1q21.1 region in an independent sample of 788 patients with mental retardation and congenital anomalies. CONCLUSIONS: We have identified recurrent molecular lesions that elude syndromic classification and whose disease manifestations must be considered in a broader context of development as opposed to being assigned to a specific disease. Clinical diagnosis in patients with these lesions may be most readily achieved on the basis of genotype rather than phenotype.

Published
2008

45. Fen1 does not control somatic hypermutability of the (CTG)(n)*(CAG)(n) repeat in a knock-in mouse model for DM1.

Author

Broek, W.J.A.A. van den, Nelen, M.R., Heijden, G.W. van der, Wansink, D.G., Wieringa, B., Broek, W.J.A.A. van den, Nelen, M.R., Heijden, G.W. van der, Wansink, D.G., and Wieringa, B.

Abstract

Contains fulltext : 49344.pdf (publisher's version ) (Closed access), The mechanism of trinucleotide repeat expansion, an important cause of neuromuscular and neurodegenerative diseases, is poorly understood. We report here on the study of the role of flap endonuclease 1 (Fen1), a structure-specific nuclease with both 5' flap endonuclease and 5'-3' exonuclease activity, in the somatic hypermutability of the (CTG)(n)*(CAG)(n) repeat of the DMPK gene in a mouse model for myotonic dystrophy type 1 (DM1). By intercrossing mice with Fen1 deficiency with transgenics with a DM1 (CTG)(n)*(CAG)(n) repeat (where 104n110), we demonstrate that Fen1 is not essential for faithful maintenance of this repeat in early embryonic cleavage divisions until the blastocyst stage. Additionally, we found that the frequency of somatic DM1 (CTG)(n)*(CAG)(n) repeat instability was essentially unaltered in mice with Fen1 haploinsufficiency up to 1.5 years of age. Based on these findings, we propose that Fen1, despite its role in DNA repair and replication, is not primarily involved in maintaining stability at the DM1 locus.

Published
2006

46. Somatic expansion behaviour of the (CTG)n repeat in myotonic dystrophy knock-in mice is differentially affected by Msh3 and Msh6 mismatch-repair proteins.

Author

Broek, W.J.A.A. van den, Nelen, M.R., Wansink, D.G., Coerwinkel, M.M., Riele, H. te, Groenen, P.J.T.A., Wieringa, B., Broek, W.J.A.A. van den, Nelen, M.R., Wansink, D.G., Coerwinkel, M.M., Riele, H. te, Groenen, P.J.T.A., and Wieringa, B.

Abstract

Item does not contain fulltext, The mechanism of expansion of the (CTG)n repeat in myotonic dystrophy (DM1) patients and the cause of its pathobiological effects are still largely unknown. Most likely, long repeats exert toxicity at the level of nuclear RNA transport or splicing. Here, we analyse cis- and trans-acting parameters that determine repeat behaviour in novel mouse models for DM1. Our mice carry 'humanized' myotonic dystrophy protein kinase (Dmpk) allele(s) with either a (CTG)84 or a (CTG)11 repeat, inserted at the correct position into the endogenous DM locus. Unlike in the human situation, the (CTG)84 repeat in the syntenic mouse environment was relatively stable during intergenerational segregation. However, somatic tissues showed substantial repeat expansions which were progressive upon aging and prominent in kidney, and in stomach and small intestine, where it was cell-type restricted. Other tissues examined showed only marginal size changes. The (CTG)11 allele was completely stable, as anticipated. Introducing the (CTG)84 allele into an Msh3-deficient background completely blocked the somatic repeat instability. In contrast, Msh6 deficiency resulted in a significant increase in the frequency of somatic expansions. Competition of Msh3 and Msh6 for binding to Msh2 in functional complexes with different DNA mismatch-recognition specificity may explain why the somatic (CTG)n expansion rate is differentially affected by ablation of Msh3 and Msh6.

Published
2002

47. A Molecular Genetic Study on Cowden Disease.

Author

Padberg, G.W.A.M., Kremer, J.M.J., Nelen, M.R., Padberg, G.W.A.M., Kremer, J.M.J., and Nelen, M.R.

Abstract

Katholieke Universiteit Nijmegen, 12 december 2000, Promotor : Padberg, G.W.A.M. Co-promotor : Kremer, J.M.J., Item does not contain fulltext

Published
2000

50. Novel PTEN mutations in patients with Cowden disease: absence of clear genotype-phenotype correlations.

Author

Nelen, M.R., Kremer, J.M.J., Konings, I.B.M., Schoute, F., Essen, A.J. van, Koch, R., Woods, C.G., Fryns, J.P., Hamel, B.C.J., Hoefsloot, L.H., Peeters, E.A.J., Padberg, G.W.A.M., Nelen, M.R., Kremer, J.M.J., Konings, I.B.M., Schoute, F., Essen, A.J. van, Koch, R., Woods, C.G., Fryns, J.P., Hamel, B.C.J., Hoefsloot, L.H., Peeters, E.A.J., and Padberg, G.W.A.M.

Abstract

Item does not contain fulltext

Published
1999

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