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 1

Gene Patients with mutation (n = 96) 
ATM 14 14.58% 
BARD1 7.29% 
BRIP1 7.29% 
CHEK2 30 31.25% 
MSH2 2.08% 
MSH6 2.08% 
MUTYH 1.04% 
NBN 14 14.58% 
PALB2 13 13.54% 
PMS2 4.17% 
TP53 2.08% 
Gene Patients with mutation (n = 96) 
ATM 14 14.58% 
BARD1 7.29% 
BRIP1 7.29% 
CHEK2 30 31.25% 
MSH2 2.08% 
MSH6 2.08% 
MUTYH 1.04% 
NBN 14 14.58% 
PALB2 13 13.54% 
PMS2 4.17% 
TP53 2.08% 

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 2

Patient Cancer History Patients (n) BRCA1/2 Other Gene 
Breast CA < 50 years 1091 116* (10.63%) 51 (4.67%) 
Breast CA ≥ 50 years 647 40** (6.18%) 30 (4.64%) 
Ovarian CA 162 17 (10.49%) 6 (3.70%) 
Breast and Ovarian CA 40 8 (20.00%) 4 (10.00%) 
Other HBOC Cancer 15 1 (6.67%) 2 (13.33%) 
Patient Cancer History Patients (n) BRCA1/2 Other Gene 
Breast CA < 50 years 1091 116* (10.63%) 51 (4.67%) 
Breast CA ≥ 50 years 647 40** (6.18%) 30 (4.64%) 
Ovarian CA 162 17 (10.49%) 6 (3.70%) 
Breast and Ovarian CA 40 8 (20.00%) 4 (10.00%) 
Other HBOC Cancer 15 1 (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.