Full BRCA coverage to detect pathogenic variants by NGS

Published Tue Mar 20, 2018

The Archer® VariantPlex® BRCA assays are robust target enrichment panels for next-generation sequencing (NGS) that simultaneously detect and characterize all known germline and somatic mutations in both BRCA1 and BRCA2 as well as PALB2. The power behind VariantPlex assays lies in Archer’s proprietary Anchored Multiplex PCR™-based enrichment of regions of interest, which enables high-confidence detection of all mutation types from a single sequencing assay. Combined with an easy-to-use lyophilized workflow and an intuitive, comprehensive bioinformatics platform, VariantPlex NGS assays eliminate the bottlenecks associated with comprehensive mutation detection in these cancer susceptibility genes.

Superior coverage

VariantPlex assay designs provide high-confidence coverage of all coding and non-coding exons in RefSeq-annotated transcript models for these genes. As shown in the images below, AMP-enabled enrichment of targeted regions using molecular barcoded adapters amplifies each DNA strand independently and bi-directionally. Unique, de-duplicated sequencing reads corresponding to the input DNA fragments input is a unique feature of VariantPlex chemistry. This provides true quantitative sample depth unlike total raw sequencing depth associated with traditional amplicon-based target enrichment – which cannot be correlated to true genomic sampling depth.

Full coverage of BRCA 1

Screenshot shows representative coverage of BRCA1
Percent of bases covered
Unique fragments 20X 50X 100X 200X
300K reads100%100%99.8%97.7%
500K reads100%100%100%99.3%
1M reads100%100%100%99.7%

Full coverage of PALB2

Screenshot shows representative coverage of PALB2
Percent of bases covered
Unique fragments 20X 50X 100X 200X
300K reads100%100%99.3%94.7%
500K reads100%100%100%98.7%
1M reads100%100%100%99.1%

Superior uniformity

Coverage uniformity for these VariantPlex designs exceed 99%, resulting in several benefits:

  • Maximized coverage with minimal reads per sample
  • More samples per run
  • Reduced sequencing costs
  • Maximized operational efficiency
VariantPlex BRCA1/2 Assay coverage uniformity This waterfall plot shows the proportion of targeted bases (y-axis) with unique, de-duplicated sequence coverage (x-axis) obtained using either 500,000 or 1,000,000 total reads allocated to each sample. Such detailed resolution of true sampling depth enables you to define your assay performance with high-confidence.

Mutation calling

The VariantPlex BRCA assays are engineered with primers to detect virtually all known mutations including SNVs, CNVs, insertions, and deletions. Gene variants targeted by these designs were accurately called down to 0.1% allele fraction using in silico generated NGS reads.


BRCA1, BRCA2 and PALB2 are human genes that play important roles maintaining genomic stability by promoting repair of double-strand DNA breaks1. Mutations in BRCA1, BRCA2 or PALB2 genes can prevent protein translation or result in protein misfunction. DNA repair is thus affected, resulting in genetic alterations that lead to oncogenesis2.

Breast and ovarian cancer risks

Inherited BRCA1/2 mutations substantially increase the lifetime risk of developing breast and/or ovarian cancer. Within the general population, the lifetime risk of developing breast cancer is about 12%. If BRCA1 or BRCA2 mutations are inherited, this risk increases to 55-65% and 45%, respectively3. BRCA1-related breast cancers are more likely to fall in the category of triple-negative breast cancer (TNBC) (i.e., estrogen and progesterone receptor-negative and with no HER2/nue overexpression)4, resulting in lack of response to hormonal therapy or targeted therapies against HER2. While most TNBC are difficult to treat, there is evidence suggesting TNBC patients with BRCA1/2 mutations have significantly dimished risk of disease recurrence6.

Like breast cancer, ovarian cancer risk increases with BRCA1/2 mutations. Within the general population, the lifetime risk of developing ovarian cancer is 1.4%. If a BRCA1 or BRCA2 mutation is inherited, this risk increases to 39% or 11-17%, respectively. Individuals with an inherited mutation in PALB2 may have a nine-fold greater risk of developing breast cancer before age 405. Recently, there has been activity related to drug development for breast and ovarian cancer patients with BRCA1/2 mutations7. The recently approved PARP inhibitors hold great promise, as these inhibitors are specifically toxic to cells with BRCA1/2 mutations8. This is primarily because inhibition of PARP results in the accumulation of double-stand DNA breaks, which cannot be repaired without BRCA1/2.

Breast cancer incidence rates infographic Ovarian cancer incidence rates infographic

Other cancer risks

In addition to breast and ovarian cancer, BRCA1/2 mutations are associated with fallopian tube cancer and peritoneal cancer9. Men with mutations are at increased risk of male breast cancer and prostate cancer10, and evidence also suggests that both sexes are at increased risk of pancreatic cancer11.

Learn more about Archer panels for inherited diseases


  1. Gudmundsdottir K, Ashworth A. The roles of BRCA1 and BRCA2 and associated proteins in the maintenance of genomic stability. Oncogene. 2006;25(43):5864–5874. doi:10.1038/sj.onc.1209874.
  2. BRCA1 and BRCA2: Cancer Risk and Genetic Testing, National Cancer Institute http://www.cancer.gov/cancertopics
    . Accessed 27 February 2015.
  3. Howlader N, Noone AM, Krapcho M, Garshell J, Neyman N, Altekruse SF, Kosary CL, Yu M, Ruhl J, Tatalovich Z, Cho H, Mariotto A, Lewis DR, Chen HS, Feuer EJ, Cronin KA (eds). SEER Cancer Statistics Review, 1975-2010, National Cancer Institute. Bethesda, MD, http://seer.cancer.gov/csr/1975_2010/, based on November 2012 SEER data submission, posted to the SEER web site, April 2013.
  4. Chen S, Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007;25(11):1329–1333. doi:10.1200/JCO.2006.09.1066.
  5. Antoniou AC, Casadei S, Heikkinen T, et al., Breast-Cancer Risk in Families with Mutations in PALB2. N Engl J Med. 2014;371:497-506. Doi:10.1056/NEJMoa1200382
  6. Gonzalez-Angulo AM, Timms KM, Liu S, et al. Incidence and outcome of BRCA mutations in unselected patients with triple receptor-negative breast cancer. Clinical Cancer Research. 2011;17(5):1082–1089. doi:10.1158/1078-0432.CCR-10-2560.
  7. FDA News Release: FDA approves Lynparza to treat advanced ovarian cancer http://www.fda.gov/
    . Accessed 27 February 2015.
  8. Dziadkowiec KN, Gqsiorowska E, Nowak-Markwitz E, Jankowska A. PARP inhibitors: review of mechanisms of action and BRCA1/2 mutation targeting. Menopause Review. 2016;15(4):215-219. doi: 10.5114/pm.2016.65667.
  9. Brose MS, Rebbeck TR, Calzone KA, Stopfer JE, Nathanson KL, Weber BL. Cancer risk estimates for BRCA1 mutation carriers identified in a risk evaluation program. JNCI J Natl Cancer Inst. 2002;94(18):1365–1372. doi:10.1093/jnci/94.18.1365.
  10. Tai YC, Domchek S, Parmigiani G, Chen S. Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. JNCI J Natl Cancer Inst. 2007;99(23):1811–1814. doi:10.1093/jnci/djm203.
  11. Ferrone CR, Levine DA, Tang LH, et al. BRCA germline mutations in Jewish patients with pancreatic adenocarcinoma. J Clin Oncol. 2009;27(3):433–438. doi:10.1200/JCO.2008.18.5546.

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For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.