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2. Whole-exome sequencing of a pedigree segregating asthma

Author

DeWan, Andrew T, Egan, Kathryn Brigham, Hellenbrand, Karen, Sorrentino, Keli, Pizzoferrato, Nicole, Walsh, Kyle M, and Bracken, Michael B

Abstract

Abstract Background Despite the success of genome-wide association studies for asthma, few, if any, definitively causal variants have been identified and there is still a substantial portion of the heritability of the disease yet to be discovered. Some of this “missing heritability” may be accounted for by family-specific coding variants found to be segregating with asthma. Methods To identify family-specific variants segregating with asthma, we recruited one family from a previous study of asthma as reporting multiple asthmatic and non-asthmatic children. We performed whole-exome sequencing on all four children and both parents and identified coding variants segregating with asthma that were not found in other variant databases. Results Ten novel variants were identified that were found in the two affected offspring and affected mother, but absent in the unaffected father and two unaffected offspring. Of these ten, variants in three genes (PDE4DIP, CBLB, and KALRN) were deemed of particular interest based on their functional prediction scores and previously reported function or asthma association. We did not identify any common risk variants segregating with asthma, however, we did observe an increase in the number of novel, nonsynonymous variants in asthma candidate genes in the asthmatic children compared to the non-asthmatic children. Conclusions This is the first report applying exome sequencing to identify asthma susceptibility variants. Despite having sequenced only one family segregating asthma, we have identified several potentially functional variants in interesting asthma candidate genes. This will provide the basis for future work in which more families will be sequenced to identify variants across families that cluster within genes.

Published
2012

3. Genome-wide association study identifies a maternalcopy-number deletion in PSG11 enriched amongpreeclampsia patients

Author

Zhao, Linlu, Triche, Elizabeth W, Walsh, Kyle M, Bracken, Michael B, Saftlas, Audrey F, Hoh, Josephine, and Dewan, Andrew T

Abstract

AbstractBackgroundSpecific genetic contributions for preeclampsia (PE) are currently unknown. This genome-wide association study (GWAS) aims to identify maternal single nucleotide polymorphisms (SNPs) and copy-number variants (CNVs) involved in the etiology of PE.MethodsA genome-wide scan was performed on 177 PE cases (diagnosed according to National Heart, Lung and Blood Institute guidelines) and 116 normotensive controls. White female study subjects from Iowa were genotyped on Affymetrix SNP 6.0 microarrays. CNV calls made using a combination of four detection algorithms (Birdseye, Canary, PennCNV, and QuantiSNP) were merged using CNVision and screened with stringent prioritization criteria. Due to limited DNA quantities and the deleterious nature of copy-number deletions, it was decided a priori that only deletions would be selected for assay on the entire case-control dataset using quantitative real-time PCR.ResultsThe top four SNP candidates had an allelic or genotypic p-value between 10-5 and 10-6, however, none surpassed the Bonferroni-corrected significance threshold. Three recurrent rare deletions meeting prioritization criteria detected in multiple cases were selected for targeted genotyping. A locus of particular interest was found showing an enrichment of case deletions in 19q13.31 (5/169 cases and 1/114 controls), which encompasses the PSG11 gene contiguous to a highly plastic genomic region. All algorithm calls for these regions were assay confirmed.ConclusionsCNVs may confer risk for PE and represent interesting regions that warrant further investigation. Top SNP candidates identified from the GWAS, although not genome-wide significant, may be useful to inform future studies in PE genetics.

Published
2012

5. Complement Factor H Polymorphism in Age-Related Macular Degeneration

Author

Klein, Robert J., Zeiss, Caroline, Chew, Emily Y., Tsai, Jen-Yue, Sackler, Richard S., Haynes, Chad, Henning, Alice K., SanGiovanni, John Paul, Mane, Shrikant M., Mayne, Susan T., Bracken, Michael B., Ferris, Frederick L., Ott, Jurg, Barnstable, Colin, and Hoh, Josephine

Published
2005

18. Response

Author

Playdon, Mary C., Bracken, Michael B., Sanft, Tara B., Ligibel, Jennifer A., Harrigan, Maura, and Irwin, Melinda L.

Published
2016
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20. Associations of Maternal Vitamin B12 Concentration in Pregnancy With the Risks of Preterm Birth and Low Birth Weight: A Systematic Review and Meta-Analysis of Individual Participant Data

Author

Rogne, Tormod, Tielemans, Myrte J., Chong, Mary Foong-Fong, Yajnik, Chittaranjan S., Krishnaveni, Ghattu V., Poston, Lucilla, Jaddoe, Vincent W. V., Steegers, Eric A. P., Joshi, Suyog, Chong, Yap-Seng, Godfrey, Keith M., Yap, Fabian, Yahyaoui, Raquel, Thomas, Tinku, Hay, Gry, Hogeveen, Marije, Demir, Ahmet, Saravanan, Ponnusamy, Skovlund, Eva, Martinussen, Marit P., Jacobsen, Geir W., Franco, Oscar H., Bracken, Michael B., and Risnes, Kari R.

Published
2017
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37. When Can Odds Ratios Mislead?

Author

Deeks, Jon, Bracken, Michael B., Sinclair, John C., Davies, Huw Talfryn Oakley, Tavakoli, Manouche, and Crombie, Iain Kinloch

Published
1998

48. Maternal anthropometric factors and risk of primary cesarean delivery

Author

Shephard, Mary Jo, Saftlas, Audrey F., Leo-Summers, Linda, and Bracken, Michael B.

Subjects
Pregnant women -- Weight gain, Cesarean section -- Risk factors, Government, Health care industry
Abstract

Objectives. This study examined absolute and proportional gestational weight gain and prepregnancy body mass index as predictors of primary cesarean delivery. Methods. Data were derived from a prospective study of pregnancy outcome risk factors in 2301 women in greater New Haven, Conn, who had singleton deliveries by primary cesarean (n = 312) or vaginal delivery (n = 1989) and for whom height, prepregnancy weight, and weight gain were available. Women were divided into 4 body mass index groups (underweight, low average, high average, and obese) and further subdivided into 8 groups according to median proportional or absolute weight gain. Results. Risk of cesarean delivery increased with increasing body mass index and gestational weight gain greater than the median for one's body mass index. Proportional weight gain was more predictive of cesarean delivery than absolute weight gain. Underweight women gaining more than 27.8% of their prepregnancy weight had a 2-tbld adjusted relative risk of cesarean delivery. Conclusions. Proportional weight gain is an important predictor of cesarean delivery for underweight women; high body mass index is also predictive of increased risk. (Am J Public Health. 1998;88:1534 1538)

Published
1998

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