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PURPOSE Screening and prevention decisions for women at increased risk of developing breast cancer depend on genetic and clinical factors to estimate risk and select appropriate interventions. Integration of polygenic risk into clinical breast cancer risk estimators can improve discrimination. However, correlated genetic effects must be incorporated carefully to avoid overestimation of risk. MATERIALS AND METHODS A novel Fixed-Stratified method was developed that accounts for confounding when adding a new factor to an established risk model. A combined risk score (CRS) of an 86–single-nucleotide polymorphism polygenic risk score and the Tyrer-Cuzick v7.02 clinical risk estimator was generated with attenuation for confounding by family history. Calibration and discriminatory accuracy of the CRS were evaluated in two independent validation cohorts of women of European ancestry (N = 1,615 and N = 518). Discrimination for remaining lifetime risk was examined by age-adjusted logistic regression. Risk stratification with a 20% risk threshold was compared between CRS and Tyrer-Cuzick in an independent clinical cohort (N = 32,576). RESULTS Simulation studies confirmed that the Fixed-Stratified method produced accurate risk estimation across patients with different family history. In both validation studies, CRS and Tyrer-Cuzick were significantly associated with breast cancer. In an analysis with both CRS and Tyrer-Cuzick as predictors of breast cancer, CRS added significant discrimination independent of that captured by Tyrer-Cuzick ( P < 10−11 in validation 1; P < 10−7 in validation 2). In an independent cohort, 18% of women shifted breast cancer risk categories from their Tyrer-Cuzick–based risk compared with risk estimates by CRS. CONCLUSION Integrating clinical and polygenic factors into a risk model offers more effective risk stratification and supports a personalized genomic approach to breast cancer screening and prevention.

Background: Germline pathogenic variants (PVs) in the moderate penetrance ATM gene confer a roughly 2-fold increased risk for breast cancer. Currently, any woman with an ATM PV meets the >20% lifetime risk threshold for consideration of relatively aggressive screening recommendations, which include initiating screening at younger ages and consideration of breast MRI. We and others have previously shown that breast cancer risks for women with inherited PVs in many hereditary breast cancer genes can be adjusted using PRS data, breast cancer family history, and other clinical information. Herein we show the development of a comprehensive breast cancer risk model for ATM PV carriers incorporating a previously described 86-variant PRS along with family history/clinical information captured by Tyrer-Cuzick V7.02. Methods: This IRB-approved study included de-identified clinical records from 353,809 women of European ancestry who were tested clinically for hereditary cancer risk with a multi-gene panel. Model development analyzed ATM PV carriers (N=2,666) and women negative for breast cancer gene PVs (N=351,143) who were tested between September 2013 and November 2019 (July 2019 for non-carriers). Women with the unusually high risk ATM c.7271 allele were excluded from analysis. Risk estimates incorporating ATM, PRS, and Tyrer-Cuzick were calculated using a fixed-stratified method that accounted for correlations between risk factors in a manner equivalent to multivariable co-estimation. Risk stratification was assessed in an independent cohort of ATM carriers (N=272) who were tested after November 2019 and were not included in model development. Results: We detected significant positive correlation of ATM status with breast cancer family history (p=1.6×10−7). Within ATM PV carriers, we observed positive yet non-significant (at alpha 50%). Conclusions: In ATM PV carriers, our comprehensive model allowed for differentiation of ATM PV carriers into low, moderate, and high breast cancer risk categories. Precision breast cancer risk estimation may inform individualized clinical screening and prevention strategies. Citation Format: Shannon Gallagher, Elisha Hughes, Eric Rosenthal, Allison W. Kurian, Susan Domchek, Judy Garber, Braden Probst, Brian Morris, Placede Tshiaba, Benjamin Roa, Thomas P. Slavin, Susanne Wagner, Jeffrey N. Weitzel, Alexander Gutin, Jerry S. Lanchbury, Mark E. Robson. Development of a breast cancer risk assessment model for ATM mutation carriers incorporating tyrer-cuzick and a polygenic risk score (PRS) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD10-09.

PURPOSE Women with a family history of breast cancer are frequently referred for hereditary cancer genetic testing, yet < 10% are found to have pathogenic variants in known breast cancer susceptibility genes. Large-scale genotyping studies have identified common variants (primarily single-nucleotide polymorphisms [SNPs]) with individually modest breast cancer risk that, in aggregate, account for considerable breast cancer susceptibility. Here, we describe the development and empirical validation of an SNP-based polygenic breast cancer risk score. METHODS A panel of 94 SNPs was examined for association with breast cancer in women of European ancestry undergoing hereditary cancer genetic testing and negative for pathogenic variants in breast cancer susceptibility genes. Candidate polygenic risk scores (PRSs) as predictors of personal breast cancer history were developed through multivariable logistic regression models adjusted for age, cancer history, and ancestry. An optimized PRS was validated in 2 independent cohorts (n = 13,174; n = 141,160). RESULTS Within the training cohort (n = 24,259), 4,291 women (18%) had a personal history of breast cancer and 8,725 women (36%) reported breast cancer in a first-degree relative. The optimized PRS included 86 variants and was highly predictive of breast cancer status in both validation cohorts ( P = 6.4 × 10−66; P < 10−325). The odds ratio (OR) per unit standard deviation was consistent between validations (OR, 1.45 [95% CI, 1.39 to 1.52]; OR 1.47 [95% CI, 1.45 to 1.49]). In a direct comparison, the 86-SNP PRS outperformed a previously described PRS of 77 SNPs. CONCLUSION The validation and implementation of a PRS for women without pathogenic variants in known breast cancer susceptibility genes offers potential for risk stratification to guide surveillance recommendations.

PURPOSE Breast cancer risks for CHEK2 and ATM pathogenic variant (PV) carriers are modified by an 86-single nucleotide polymorphism polygenic risk score (PRS) and individual clinical factors. Here, we describe comprehensive risk prediction models for women of European ancestry combining PV status, PRS, and individual clinical variables. MATERIALS AND METHODS This study included deidentified clinical records from 358,095 women of European ancestry who received testing with a multigene panel (September 2013 to November 2019). Model development included CHEK2 PV carriers (n = 4,286), ATM PV carriers (n = 2,666), and women negative for other breast cancer risk gene PVs (n = 351,143). Odds ratios (ORs) were calculated using multivariable logistic regression with adjustment for familial cancer history. Risk estimates incorporating PV status, PRS, and Tyrer-Cuzick v7.02 were calculated using a Fixed-Stratified method that accounts for correlations between risk factors. Stratification of PV carriers into risk categories on the basis of remaining lifetime risk (RLR) was assessed in independent cohorts of PV carriers. RESULTS ORs for association of PV status with breast cancer were 2.01 (95% CI, 1.88 to 2.16) and 1.83 (95% CI, 1.68 to 2.00) for CHEK2 and ATM PV carriers, respectively. ORs for PRS per one standard deviation were 1.51 (95% CI, 1.37 to 1.66) and 1.45 (95% CI, 1.30 to 1.64) in CHEK2 and ATM PV carriers, respectively. Using the combined model (PRS plus Tyrer-Cuzick plus PV status), RLR was low (≤ 20%) for 24.2% of CHEK2 PV carriers, medium (20%-50%) for 63.8%, and high (> 50%) for 12.0%. Among ATM PV carriers, RLR was low for 31.5% of patients, medium for 58.5%, and high for 9.7%. CONCLUSION In CHEK2 and ATM PV carriers, risk assessment including PRS, Tyrer-Cuzick, and PV status has the potential for more precise direction of screening and prevention strategies.

Background: The incorporation of polygenic scores into breast cancer risk assessment models has led to improved risk management for women of European ancestry. However, few studies have examined the extent to which polygenic scores modify risk for carriers of breast cancer susceptibility gene mutations. Current literature suggests that a 77-SNP polygenic score developed from large, mainly non-carrier general population studies can stratify breast cancer risk for carriers of the CHEK2 founder mutation 1100delC with the same effect size observed for non-carriers. Consequently, several groups have modified risk estimates for carriers of other pathogenic variants by applying published effect estimates from non-carriers. In a recent study, a similar 88-SNP polygenic score showed reduced effectiveness in BRCA1 and BRCA2 carriers compared to non-carriers. This highlights the need for more information on polygenic score performance among women who carry pathogenic variants in ATM or PALB2, or in CHEK2 other than the 1100delC founder mutation. We previously described an 86-SNP polygenic residual risk score (RRS) that characterizes genetic risk which is not due to high- or moderate-penetrance breast cancer gene mutations. Here, we present pre-specified independent validation of the RRS for BRCA1, BRCA2, CHEK2, ATM and PALB2 carriers.Methods: This IRB-approved study included 152,172 women of European ancestry who were tested clinically for hereditary cancer risk with a multi-gene panel. The RRS was evaluated separately for carriers of BRCA1 (N=2,249), BRCA2 (N=2,638), CHEK2 (N=2,564), ATM (N=1,445) and PALB2 (N=906), and for mutation-free women (N=141,160). Clinical information was obtained from test requisition forms. Multivariable logistic regression was used to examine the association of RRS with invasive breast cancer after accounting for age and family cancer history. Effect sizes, expressed as standardized odds ratios (ORs) with 95% confidence intervals (CIs), were assessed for carriers of each gene and for non-carriers. Results: RRS was strongly associated with breast cancer risk in each of the BRCA1, BRCA2, CHEK2, ATM and PALB2 carrier populations (p Citation Format: Shannon Gallagher, Elisha Hughes, Susanne Wagner, Placede Tshiaba, Eric Rosenthal, Benjamin B. Roa, Allison Kurian, Susan Domchek, Judy Garber, Johnathan M. Lancaster, Jeffrey Weitzel, Alexander Gutin, Jerry S. Lanchbury, Mark Robson. Polygenic breast cancer risk modification in carriers of high and intermediate risk gene mutations [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-07.

Expanded genetic test utilization to guide cancer management has driven the development of larger gene panels and greater diversity in the patient population pursuing testing, resulting in increased identification of atypical or technically challenging genetic findings. To ensure appropriate patient care, it is critical that genetic tests adequately identify and characterize these findings. We describe genetic testing challenges frequently encountered by our laboratory and the methodologies we employ to improve test accuracy for the identification and characterization of atypical genetic findings. While these findings may be individually rare, 15,745 (9%) individuals tested by our laboratory for hereditary cancer risk had an atypical genetic finding, highlighting the importance of employing highly accurate and comprehensive methods in clinical genetic testing.

IMPORTANCE: To date, few studies have examined the extent to which polygenic single-nucleotide variation (SNV) (formerly single-nucleotide polymorphism) scores modify risk for carriers of pathogenic variants (PVs) in breast cancer susceptibility genes. In previous reports, polygenic risk modification was reduced for BRCA1 and BRCA2 PV carriers compared with noncarriers, but limited information is available for carriers of CHEK2, ATM, or PALB2 PVs. OBJECTIVE: To examine an 86-SNV polygenic risk score (PRS) for BRCA1, BRCA2, CHEK2, ATM, and PALB2 PV carriers. DESIGN, SETTING, AND PARTICIPANTS: A retrospective case-control study using data on 150 962 women tested with a multigene hereditary cancer panel between July 19, 2016, and January 11, 2019, was conducted in a commercial testing laboratory. Participants included women of European ancestry between the ages of 18 and 84 years. MAIN OUTCOMES AND MEASURES: Multivariable logistic regression was used to examine the association of the 86-SNV score with invasive breast cancer after adjusting for age, ancestry, and personal and/or family cancer history. Effect sizes, expressed as standardized odds ratios (ORs) with 95% CIs, were assessed for carriers of PVs in each gene as well as for noncarriers. RESULTS: The median age at hereditary cancer testing of the population was 48 years (range, 18-84 years); there were 141 160 noncarriers in addition to carriers of BRCA1 (n = 2249), BRCA2 (n = 2638), CHEK2 (n = 2564), ATM (n = 1445), and PALB2 (n = 906) PVs included in the analysis. The 86-SNV score was associated with breast cancer risk in each of the carrier populations (P

1504 Background: Women with pathogenic variants in the moderate penetrance CHEK2 gene have on average an estimated > 20% lifetime risk for breast cancer, thereby meeting an established threshold for more aggressive screening, including consideration of breast magnetic resonance imaging (MRI). However, we previously showed that CHEK2 penetrance is modified by an 86-SNP PRS. CHEK2 risk is further modified by family history (FH) and other TC model variables. Here, we describe development of a comprehensive risk prediction model for women of European ancestry to more precisely estimate risk by incorporating CHEK2, PRS and TC V7.02. The number of CHEK2 carriers with low ( < 20%), moderate (20%-50%) and high ( > 50%) remaining lifetime risk based on the combined model was examined in an independent study cohort. Methods: This IRB-approved study included de-identified clinical records from 358,471 women of European ancestry who were tested clinically for hereditary cancer risk with a multi-gene panel. Model development was based on analysis of CHEK2 PV carriers ( N= 4,331) and women negative for BC gene PV ( N =353,681) who were tested between September 2013 and July 2019. Risk estimates incorporating CHEK2, PRS and TC were calculated using a fixed-stratified (FS) method that accounts for correlations between risk factors in a manner equivalent to multivariable co-estimation. Risk stratification was assessed in an independent cohort of CHEK2 carriers ( N= 459) who were tested after July 2019 and not included in model development. Results: We detected significant correlation of CHEK2 status with FH ( p= 4.1 × 10−17) and of PRS with FH among CHEK2 carriers ( p= 1.7× 10−5). For these factors, joint effects were co-estimated using the FS method. In an independent cohort, 24.0% of CHEK2 carriers were categorized as low risk ( < 20%), and 62.6% were categorized as moderate risk (20-50%). For 13.4% of CHEK2 carriers, risk estimation incorporating PRS and TC generated BC risks of greater than 50%, consistent with genes recognized as highly penetrant. Conclusions: In CHEK2 PV carriers, comprehensive risk assessment could inform individualized decision-making and may lead to improved targeting of screening and prevention strategies.

BACKGROUND Next-generation sequencing (NGS) allows for simultaneous sequencing of multiple cancer susceptibility genes and, for an individual, may be more efficient and less expensive than sequential testing. The authors assessed the frequency of deleterious germline mutations among individuals with breast cancer who were referred for BRCA1 and BRCA2 (BRCA1/2) gene testing using a panel of 25 genes associated with inherited cancer predisposition. METHODS This was a cross-sectional study using NGS in 2158 individuals, including 1781 who were referred for commercial BRCA1/2 gene testing (cohort 1) and 377 who had detailed personal and family history and had previously tested negative for BRCA1/2 mutations (cohort 2). RESULTS Mutations were identified in 16 genes, most frequently in BRCA1, BRCA2, CHEK2, ATM, and PALB2. Among the participants in cohort 1, 9.3% carried a BRCA1/2 mutation, 3.9% carried a mutation in another breast/ovarian cancer susceptibility gene, and 0.3% carried an incidental mutation in another cancer susceptibility gene unrelated to breast or ovarian cancer. In cohort 2, the frequency of mutations in breast/ovarian-associated genes other than BRCA1/2 was 2.9%, and an additional 0.8% had an incidental mutation. In cohort 1, Lynch syndrome-related mutations were identified in 7 individuals. In contrast to BRCA1/2 mutations, neither age at breast cancer diagnosis nor family history of ovarian or young breast cancer predicted for other mutations. The frequency of mutations in genes other than BRCA1/2 was lower in Ashkenazi Jews compared with non-Ashkenazi individuals (P=.026). CONCLUSIONS Using an NGS 25-gene panel, the frequency of mutations in genes other than BRCA1/2 was 4.3%, and most mutations (3.9%) were identified in genes associated with breast/ovarian cancer. Cancer 2015;121:25–33. © 2014 American Cancer Society.

BACKGROUND This study sought to determine the prevalence of PALB2 mutations in a cohort referred for diagnostic testing for hereditary breast cancer. METHODS Sanger sequencing was used to analyze the entire coding region and flanking introns of PALB2 in anonymized DNA samples from 1479 patients. Samples were stratified into a “high-risk” group, 955 samples from individuals predicted to have a high probability of carrying a mutation in BRCA1 or BRCA2 based on their personal and family history, and a “lower-risk” group consisting of 524 samples from patients with breast cancer, but fewer risk factors for being a BRCA1 or BRCA2 mutation carrier. All patients were known to be negative for deleterious sequence mutations and large rearrangements in BRCA1 and BRCA2. RESULTS We identified 12 disease-associated PALB2 mutations among the 1479 patients (0.8%). The PALB2 mutations included 8 nonsense, 3 frameshift mutations and a splice-site mutation. The mutation prevalence for the high-risk population was 1.05% (95% CI = 0.5-1.92), whereas that for the lower-risk population was 0.38% (95% CI = 0.05-1.37). We identified 59 PALB2 variants of uncertain significance (VUS) among 57 of the 1479 patients (3.9%). CONCLUSIONS These results suggest that PALB2 mutations occur at a frequency of ∼1% in patients with hereditary breast cancer. Cancer 2014;120:963–967. © 2013 American Cancer Society.

Identifying individuals at increased risk for hereditary cancer leads to early detection and prevention opportunities with the ability to reduce both cancer incidence and mortality. Hereditary cancer syndromes have genetic heterogeneity and new susceptibility genes have been recently identified. Next generation sequencing allows testing of multiple target genes simultaneously, can reduce the time and cost of sequential gene testing, and may improve mutation detection. To date, no large scale studies have reported the mutation prevalence of multiple cancer susceptibility genes among patients referred for BRCA1/BRCA2 testing. A study was performed to determine the mutation prevalence in 25 cancer susceptibility genes among a large U.S. patient population referred to a diagnostic laboratory for BRCA1/BRCA2 testing. DNA from 1955 prospectively accrued cases was anonymized after testing was complete. Patients with Ashkenazi Jewish heritage were excluded in order to determine the relative prevalence of mutations in a generalizable population. In addition, an independent external validation set of 405 patients, including those of Ashkenazi ancestry, with history consistent with hereditary breast and ovarian cancer (HBOC) syndrome and who had previously tested negative for BRCA1/BRCA2 mutations was assessed. Extracted genomic DNA from blood was PCR amplified with a custom amplicon library on a Raindance ThunderStorm instrument. The DNA products were sequenced on an Illumina HiSeq2500. Sequence variations and large rearrangements among the 25 genes were detected and classified for pathogenicity. Among the 1955 anonymized patients referred for BRCA1/BRCA2 testing, 275 (14.07%) patients were mutation carriers in at least one of the 25 genes. 182 (9.31%) patients had a mutation in BRCA1 or BRCA2, and 96 of 1955 (4.91%) patients had a mutation in other genes (Table 1). Table 1GenePatients with mutation (n = 96)%ATM1414.58%BARD177.29%BRIP177.29%CHEK23031.25%MSH222.08%MSH622.08%MUTYH11.04%NBN1414.58%PALB21313.54%PMS244.17%TP5322.08% No mutations were found in CDH1, PTEN, STK11, RAD51C, RAD51D, BMPR1A, SMAD4, MLH1, EPCAM, CDKN2A, CDK4, or APC. 1738 of 1955 patients had a personal history of breast cancer (BC), with 63% diagnosed prior to age 50, and 37% at or after age 50. Mutation prevalence for patients with BC, ovarian cancer (OC), both BC and OC, or other HBOC cancers is listed in Table 2. Table 2Patient Cancer HistoryPatients (n)BRCA1/2Other GeneBreast CA < 50 years1091116* (10.63%)51 (4.67%)Breast CA ≥ 50 years64740** (6.18%)30 (4.64%)Ovarian CA16217 (10.49%)6 (3.70%)Breast and Ovarian CA408 (20.00%)4 (10.00%)Other HBOC Cancer151 (6.67%)2 (13.33%)*2 and **1 patients had an additional mutation in a non-BRCA1/2 gene 1902 (97.29%) patients had a variant of uncertain significance in at least one of the genes tested and an average of three variants was found per patient. As of June 11, 2013 the independent external validation cases results are pending. Compared with BRCA1/BRCA2 testing alone, using the 25 gene panel increased the identification of mutations in cancer susceptibility genes by 4.76% (95% CI: 2.71% – 6.81%), which represents a 51.1% increase in mutation detection for this population with suspected HBOC. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD4-8.

BACKGROUND Recently, a 23‐gene signature was developed to produce a melanoma diagnostic score capable of differentiating malignant and benign melanocytic lesions. The primary objective of this study was to independently assess the ability of the gene signature to differentiate melanoma from benign nevi in clinically relevant lesions. METHODS A set of 1400 melanocytic lesions was selected from samples prospectively submitted for gene expression testing at a clinical laboratory. Each sample was tested and subjected to an independent histopathologic evaluation by 3 experienced dermatopathologists. A primary diagnosis (benign or malignant) was assigned to each sample, and diagnostic concordance among the 3 dermatopathologists was required for inclusion in analyses. The sensitivity and specificity of the score in differentiating benign and malignant melanocytic lesions were calculated to assess the association between the score and the pathologic diagnosis. RESULTS The gene expression signature differentiated benign nevi from malignant melanoma with a sensitivity of 91.5% and a specificity of 92.5%. CONCLUSIONS These results reflect the performance of the gene signature in a diverse array of samples encountered in routine clinical practice. Cancer 2017;123:617–628. © 2016 American Cancer Society., A 23‐gene signature has recently been developed to differentiate malignant and benign melanocytic lesions. This study shows that the gene expression signature differentiates benign nevi from malignant melanoma with a sensitivity of 91.5% and a specificity of 92.5% in comparison with a triple‐concordant histopathologic review.

BACKGROUND: Current estimates of the contribution of large rearrangement (LR) mutations in the BRCA1 (breast cancer 1, early onset) and BRCA2 (breast cancer 2, early onset) genes responsible for hereditary breast and ovarian cancer are based on limited studies of relatively homogeneous patient populations. The prevalence of BRCA1/2 LRs was investigated in 48,456 patients with diverse clinical histories and ancestries, referred for clinical molecular testing for suspicion of hereditary breast and ovarian cancer. METHODS: Sanger sequencing analysis was performed for BRCA1/2 and LR testing for deletions and duplications using a quantitative multiplex polymerase chain reaction assay. Prevalence data were analyzed for patients from different risk and ethnic groups between July 2007 and April 2011. Patients were designated as “high-risk” if their clinical history predicted a high prior probability, wherein LR testing was performed automatically in conjunction with sequencing. “Elective” patients did not meet the high-risk criteria, but underwent LR testing as ordered by the referring health care provider. RESULTS: Overall BRCA1/2 mutation prevalence among high-risk patients was 23.8% versus 8.2% for the elective group. The mutation profile for high-risk patients was 90.1% sequencing mutations versus 9.9% LRs, and for elective patients, 94.1% sequencing versus 5.9% LRs. This difference may reflect the bias in high-risk patients to carry mutations in BRCA1, which has a higher penetrance and frequency of LRs compared with BRCA2. There were significant differences in the prevalence and types of LRs in patients of different ancestries. LR mutations were significantly more common in Latin American/Caribbean patients. CONCLUSIONS: Comprehensive LR testing in conjunction with full gene sequencing is an appropriate strategy for clinical BRCA1/2 analysis.

Aims: The aim of these studies was to validate the analytical performance of a cell cycle progression (CCP) gene signature that provides prognostic information for early stage lung adenocarcinomas. Materials & methods: Formalin-fixed paraffin-embedded (FFPE) lung resections were evaluated by quantitative RT-PCR for the expression of 31 target and 15 housekeeper genes comprising the CCP score. Results: The signature had a standard deviation (SD) of 0.06 score units and a dynamic range spanning CCP scores between -13 and 14. The average amplicon efficiencies for target and housekeeper genes were 107% and 105%, respectively. All but one amplicon had a SD T. Conclusion: These studies demonstrate that the gene signature is robust and reproducible, making it suitable for use in a clinical setting.

Objectives Aetiological assessment of 71 probands whose clinical presentation suggested a genetic syndrome or auditory neuropathy. Methods Sanger sequencing was performed on DNA isolated from peripheral blood or lymphoblastoid cell lines. Genes were selected for sequencing based on each patient9s clinical presentation and suspected diagnosis. Observed DNA sequence variations were assessed for pathogenicity by review of the scientific literature, and mutation and polymorphism databases, through the use of in silico tools including sorting intolerant from tolerant (SIFT) and polymorphism phenotyping (PolyPhen), and according to the recommendations of the American College of Medical Genetics and Genomics for the interpretation of DNA sequence variations. Novel DNA sequence variations were sought in controls. Results DNA sequencing of the coding and near-coding regions of genes relevant to each patient9s clinical presentation revealed 37 sequence variations of known or uncertain pathogenicity in 9 genes from 25 patients. 14 novel sequence variations were discovered. Assessment of phenotypes revealed notable findings in 9 patients. Conclusions DNA sequencing in patients whose clinical presentation suggested a genetic syndrome or auditory neuropathy provided opportunities for aetiological assessment and more precise genetic counselling of patients and families. The failure to identify a genetic aetiology in many patients in this study highlights the extreme heterogeneity of genetic hearing loss, the incompleteness of current knowledge of aetiologies of hearing loss, and the limitations of conventional DNA sequencing strategies that evaluate only coding and near-coding segments of genes.

Background: Prostate cancer is the most common cancer in men in the developed world. Appropriate clinical care requires accurate prognostic information to determine whether definitive treatment or conservative management is most appropriate for a given patient. We previously demonstrated that a gene expression signature, which measures the RNA expression of 31 cell cycle progression (CCP) genes and generates a CCP score, is a robust predictor of patient outcome in cohorts of conservatively managed patients diagnosed by needle biopsy or transurethral resection of the prostate. Methods: These current studies represent the analytical validation of this gene signature, for the testing of either formalin-fixed paraffin-embedded (FFPE) prostate resection tissue (radical prostatectomy, RP) or FFPE prostate needle biopsy samples. Results: The measured standard deviation (SD) of the signature was determined to be 0.1 score units, representing 1.6% of the range of scores observed within previous clinical validation studies. Individual amplicons for all genes within the signature had a SD

Purpose: To provide a summary of the outcomes of two working conferences organized by the Centers for Disease Control and Prevention (CDC), to develop recommendations for practical, sustainable mechanisms to make quality control (QC) materials available to the genetic testing community. Methods: Participants were selected to include experts in genetic testing and molecular diagnostics from professional organizations, government agencies, industry, laboratories, academic institutions, cell repositories, and proficiency testing (PT)/external Quality Assessment (EQA) programs. Current efforts to develop QC materials for genetic tests were reviewed; key issues and areas of need were identified; and workgroups were formed to address each area of need and to formulate recommendations and next steps. Results: Recommendations were developed toward establishing a sustainable process to improve the availability of appropriate QC materials for genetic testing, with an emphasis on molecular genetic testing as an initial step. Conclusions: Improving the availability of appropriate QC materials is of critical importance for assuring the quality of genetic testing, enhancing performance evaluation and PT/EQA programs, and facilitating new test development. To meet the needs of the rapidly expanding capacity of genetic testing in clinical and public health settings, a comprehensive, coordinated program should be developed. A Genetic Testing Quality Control Materials Program has therefore been established by CDC in March 2005 to serve these needs.

Objective: We sought to establish an association between preeclampsia and the methionine to threonine polymorphism at amino acid residue 235 (Met235Thr) in angiotensinogen in a Hispanic population. We looked for a relationship between this allele and the allele in the endothelial nitric oxide synthase gene (NOS3) that produces the A form (NOS3*A) with respect to preeclampsia. Study Design: Clinical data were collected from 87 patients with preeclampsia and 53 control subjects. Patients and controls were genotyped for the angiotensinogen polymorphism allele (AGT*T) and the NOS3*A polymorphism. We then compared patients with preeclampsia and control subjects and investigated disease severity within the preeclampsia group as a function of genotype. Results: The AGT*T allelic frequencies among patients with preeclampsia and control subjects were 0.72 and 0.70, respectively ( P = .84). The blood pressure of patients with an AGT*T allele who also carried a NOS3*A allele was higher at earlier gestational ages ( r = –0.052; P = .02). Analysis suggested that the systolic blood pressure differences were due to gestational age effects and the presence of a NOS3*A allele ( P Conclusion: The AGT*T allele was not associated with the development of preeclampsia. Independently of the presence of an AGT*T allele, the NOS3*A allele was associated with a higher blood pressure at an earlier gestational age. (Am J Obstet Gynecol 2001;184:1345-51.)

Molecular laboratory techniques are increasingly important in the evaluation of fetuses at risk for a single gene disorder or chromosomal abnormality and for the detection of genetic or other conditions that can lead to an adverse fetal or maternal outcome. The localization and identification of novel disease genes allows for mutation analysis or linkage studies on fetuses at risk for these disorders. New assays or techniques for mutation detection in single gene disorders such as amplification refractory mutation system polymerase chain reaction, fluorescent polymerase chain reaction, heteroduplex analysis and the protein truncation test are now applied in prenatal diagnosis. Recent advances in molecular cytogenetics, such as comparative genomic hybridization, the primed in-situ labeling technique, the development of new telomeric probes and spectral karyotyping, are being evaluated for their role in the prenatal diagnosis of chromosomal abnormalities. These methods may greatly improve the accuracy and applicability of preimplantation genetic diagnosis or diagnosis on fetal cells isolated from maternal blood.

Charcot-Marie-Tooth disease (CMT) is an inherited disorder of the peripheral nerves, which involves slowly progressive weakness and atrophy of the distal muscles (Charcot and Marie, 1886; Tooth, 1886). CMT is a type of hereditary motor and sensory neuropathy that exhibits both clinical and genetic heterogeneity (Dyck et al., 1993; Lupski et al., 1991a). Clinical features include initial weakness of the intrinsic foot and distal leg muscles, which lead to foot deformities and gait abnormalities. Later in the course of the disease, variable progressive weakness of the hands may occur (Dyck et al. 1993; Lupski et al., 1991a). CMT constitutes the most common inherited peripheral neuropathy with an estimated population frequency of 1:2500 (Skre, 1974). Studies on the molecular genetics of CMT have provided a wealth of information in recent years, which was facilitated by parallel developments in mouse models of the disease. This brief review will summarize the current findings, paying particular attention to CMT type 1A, which is the major form of the disease. The molecular findings on CMTIA have revealed a novel mutational mechanism for an autosomal dominant human disorder. Furthermore, the gene responsible for CMTIA has been shown to be involved in two related peripheral neuropathies as well. The collective findings have furthered our understanding of the molecular bases of primary inherited peripheral neuropathies and have provided useful insights on the prospective development of strategies for gene therapy of CMT and related disorders.

Purpose: This study was designed to evaluate the feasibility of using a targeted array-CGH strategy for prenatal diagnosis of genomic imbalances in a clinical setting of current pregnancies. Methods: Women undergoing prenatal diagnosis were counseled and offered array-CGH (BCM V4.0) in addition to routine chromosome analysis. Array-CGH was performed with DNA directly from amniotic fluid cells with whole genome amplification, on chorionic villus samples with amplification as necessary, and on cultured cells without amplification. Results: Ninety-eight pregnancies (56 amniotic fluid and 42 CVS specimens) were studied with complete concordance between karyotype and array results, including 5 positive cases with chromosomal abnormalities. There was complete concordance of array results for direct and cultured cell analysis in 57 cases tested by both methods. In 12 cases, the array detected copy number variation requiring testing of parental samples for optimal interpretation. Array-CGH results were available in an average of 6 and 16 days for direct and cultured cells, respectively. Patient acceptance of array-CGH testing was 74%. Conclusion: This study demonstrates the feasibility of using array-CGH for prenatal diagnosis, including reliance on direct analysis without culturing cells. Use of array-CGH should increase the detection of abnormalities relative to the risk, and is an option for an enhanced level of screening for chromosomal abnormalities in high risk pregnancies.

Purpose: We developed a 51-mutation extended cystic fibrosis (CF) panel that incorporates the 25 previously recommended CFTR mutations, plus 26 additional mutations including 3199del6, which was associated with I148T. Methods: This assay utilizes an integrated matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system. Results: CF testing was performed on over 5,000 individuals, including a 3-year-old Hispanic-American patient with a compound heterozygous G542X/3199del6 genotype. He is negative for I148T, or other mutations assessed by CFTR gene sequencing. Conclusion: These results demonstrate the successful implementation of MALDI-TOF mass spectrometry in CF clinical testing, and establish 3199del6 as a disease-causing CF mutation.

Purpose: We expect that the mutation panel currently recommended for preconception/prenatal CF carrier screening will be modified as new information is learned regarding the phenotype associated with specific mutations and allele frequencies in various populations. One such example is the I148T mutation, originally described as a severe CF mutation. After implementation of CF population-based carrier screening, we learned that I148T exists as a complex allele with 3199del6 in patients with clinical CF, whereas asymptomatic compound heterozygotes for I148T and a second severe CF mutation were negative for 3199del6. Methods: We performed reflex testing for 3199del6 on 663 unrelated specimens, including I148T heterozygotes, compound heterozygotes, and a homozygous individual. Results: Less than 1% of I148T carriers were also positive for 3199del6. Excluding subjects tested because of a suspected or known CF diagnosis or positive family history, 0.6% of I148T-positive individuals were also positive for 3199del6. We identified 1 I148T homozygote and 6 unrelated compound heterozygous individuals with I148T and a second CF variant (2 of whom also carried 3199del6). In addition, one fetus with echogenic bowel and one infertile male were heterozygous for I148T (3199del6 negative). Conclusions: Reflex testing for 3199del6 should be considered whenever I148T is identified. Reflex testing is of particular importance for any symptomatic patient or whenever one member of a couple carries a deleterious CF mutation and the other member is an I148T heterozygote. Further population data are required to determine if I148T, in the absence of 3199del6, is associated with mild or atypical CF or male infertility. Genet Med 2004:6(5):421–425.

An 11-year-old boy was evaluated for progressive ataxia, cognitive deterioration, and ophthalmoplegia. The child initially presented with abnormal eye movements at the age of 2 months and was noted to have developmental delay at 6 months. At the age of 7 years, he developed ataxia and cognitive impairment, and subsequently manifested dysphagia and incontinence. The pertinent family history included gait difficulty in the paternal grandmother. At the age of 11, his general physical examination was normal. On neurological examination, he had bilateral external ophthalmoplegia, ataxic dysarthria, dysmetria and tremor in the upper extremities, and marked gait ataxia. An ophthalmological evaluation showed no evidence of pigmentary retinopathy. Brain MRI demonstrated cerebellar, brainstem, and cerebral atrophy. An ataxia panel showed 62 repeats in one allele of the SCA2 gene. Most cases of spinocerebellar ataxia type 2 (SCA2) present between 20 years and 40 years, and affected individuals typically have between 34 and 57 CAG repeats. Neonatal cases of SCA2 have been reported in individuals with over 200 CAG repeats. Childhood SCA2 has been reported previously in two patients but not described clinically. This case broadens the spectrum of the clinical features of infantile-onset SCA2 and highlights the importance of considering this diagnosis in infants and children.

9021 Background: Histopathologic distinction between benign and malignant melanocytic tumors can be unreliable and may lead to misdiagnosis. Measurement of biomarker gene expression has been propos...

1509 Background: Multigene panels are increasingly used for assessing hereditary cancer risk due to their ability to analyze numerous cancer susceptibility genes in parallel. Our aim was to study t...

447 Background: Dihydropyrimidine dehydrogenase (DPYD) is the major enzyme that metabolizes 5-Fluoruracil (5-FU), a component of many chemotherapy regimens. Patients with a DPYD gene mutation have higher 5-FU plasma levels, leading to a 50-60% risk of a grade 3-4 toxicity. DPYD mutations have an estimated prevalence of 3-5% in the general population, but full sequencing is rarely performed in published studies. Analyses of the largest set of full DPYD gene sequencing test results from a commercial laboratory database are presented. Methods: A set of 3,083 patients was analyzed. Patient demographics (age, gender, ethnicity) and pre-test grade 3-4 toxicity status (none, 5-FU related, other) were obtained from the test request form. Descriptive analyses were performed to estimate mutation prevalence overall, and by toxicity and ancestry classifications, as well as to characterize mutations of interest. A subset of 24 patients tested for DPYD mutations in response to high 5-FU exposure levels was also analyzed. Results: The overall DPYD mutation prevalence was 7.3%. Mutations were present in 4.7% and 10.3% of patients experiencing none and at least one 5-FU related toxicity pre-test, respectively. Among patients with toxicities pre-test, the prevalence increased from 7.8% to 31.6% for those experiencing a single to all four toxicity types. Among 5-FU related toxicities, mutation prevalence was highest (18.5%) for hematopoietic events. The previously reported founder mutation IVS14+1G>A had a relative prevalence 42.7%, but 30.9% of these mutations were seen in patients not reporting a Western/Northern European ancestry. Among the subset of patients with high 5-FU exposure levels, 29% had a DPYD mutation showing a genetic causality. Conclusions: 5-FU in chemotherapy regimens remains widespread, yet DPYD gene testing utilization remains minimal. Most testing occurs post-treatment in response to a severe toxicity rather than pre-treatment, which would permit physicians to adapt treatment and reduce toxicity risk. Compared to previous studies, this study using full sequencing data from 3083 patients provides robust estimates of DPYD mutation prevalence and helps characterize DPYD mutations of particular interest.

30 Background: PALB2 has been identified as a breast cancer susceptibility gene conferring ~ 2-4 fold increased risk of breast cancer. A number of studies have estimated the PALB2 mutation prevalence to range from 0.5% - 2.9% in populations of breast cancer patients. We performed an analysis to determine the PALB2 mutation prevalence in a large U.S. referral testing population. Methods: DNA samples were anonymized from two subsets of patients: 955 early onset breast cancer patients with severe family history, and 524 patients with later onset of breast cancer and/or less severe family history. All patients were negative for deleterious sequence mutations or large rearrangements in BRCA1 and BRCA2. Results: We identified 10 disease associated PALB2 mutations in the high risk group of 955 patients and 2 deleterious PALB2 mutations in the lower risk group of 524 patients. Identified PALB2 mutations included 8 nonsense, 3 frameshift mutations and a splice site mutation. The mutation prevalence for the high risk population was 1.05% (95% C.I., 0.5 -1.92) whereas that for the lower risk population was 0.38% (95% C.I., 0.05-1.37). The observed rate of PALB2 variants of unknown significance (VUS) identified in this study was ~5% (78 VUS were in 75 of the 1479 patients that were tested). Our variant classification program which successfully decreased the VUS rate in BRCA1 and BRCA2 is similarly expected to enhance mutation classification on an on-going basis for PALB2 genetic testing. Conclusions: Genetic testing for PALB2 may be indicated as a reflex test for breast cancer patients who test negative for BRCA1 and BRCA2.

11097 Background: Deleterious mutations in MLH1, MSH2 and MSH6 are known to cause Lynch Syndrome (HNPCC). The aim of this study was to determine the percentage of deleterious mutations represented ...

10513 Background: Mutations in the BRCA1 and BRCA2 genes are comprised of a majority of mutations that are detectable by sequence analysis, and a minority of large genomic deletion and duplication mutations that are detected by methods different than sequencing. Our laboratory developed and implemented a clinical assay for large rearrangements that we refer to as BART (BRCA1/2 Rearrangement Test). We validated the performance of BART using a completely anonymous large number of breast/ovarian cancer patient samples. We also demonstrated superior performance of BART versus other dosage-sensitive methods including Multiplex Ligation-dependent Probe Amplification (MLPA). Methods: BART utilizes quantitative endpoint polymerase chain reaction (PCR) in a multiplexed fluorescent format. Eleven multiplex PCR reactions were designed to contain two amplicons targeting the promoter region, all coding exons, and flanking regions of BRCA1 and BRCA2. An automated likelihood-based analysis application normalizes target amplicon copy number between BRCA1, BRCA2 and three control genes. Deletions and duplications are identified with a statistical confidence level. Results: Based on clinical and family history criteria, 1,035 patients were identified as severe-risk during the initial months of clinical BART analysis at Myriad Genetic Laboratories. All patients were initially tested for Comprehensive BRACAnalysis which includes BRCA1 and BRCA2 full gene sequencing plus large rearrangement panel testing for 5 recurrent BRCA1 mutations. Among severe-risk patients, 302 (29.2%) were positive for a BRCA1 or BRCA2 mutation by sequencing, 9 (0.9%) were positive by large rearrangement panel testing and an additional 27(2.6%) tested positive by BART for large genomic rearrangements. The total detection rate for deleterious mutations in severe-risk individuals was therefore 32.7%. Conclusions: Our initial clinical data indicate that BART testing is appropriate for high-risk patients identified on the basis of personal and family history criteria. No significant financial relationships to disclose.