VariantPlex BRCA1/2 Kit

The Archer® VariantPlex™ BRCA1/2 Kit is a robust targeted next-generation sequencing (NGS) assay to simultaneously detect and characterize all known germline mutations in BRCA1 and BRCA2 with full exon coverage. The power of the VariantPlex BRCA1/2 Kit lies in Archer’s proprietary Anchored Multiplex PCR™-based enrichment, which enables detection of all BRCA1 and BRCA2 variants in a single sequencing assay. Combined with an easy-to-use workflow and an intuitive, comprehensive bioinformatics platform, the VariantPlex BRCA1/2 Kit eliminates the bottlenecks associated with detecting mutations in these cancer susceptibility genes.

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

Highlights

  • Detects all known variants
  • Optimized for full exon coverage with a low number of sequencing reads

Superior Coverage

The VariantPlex BRCA1/2 Kit design covers all coding and non coding exons in RefSeq-annotated transcript models for these genes, as shown in the image below of full bi-directional coverage of BRCA2 exon 13.

VariantPlex BRCA1/2 shows full exon coverage

 

The table below shows the percent of BRCA1 and BRCA2 coding bases at various coverage depths. Increasing the number of reads per sample will allow for 100% coverage at greater depth.

Coverage depth Non-deduplicated reads Deduplicated reads
35X 100% bases covered 100% bases covered
100X 99.97% bases covered 99.75% bases covered
250X 98.48% bases covered 94.39% bases covered

Superior Uniformity

The VariantPlex BRCA1/2 Kit shows coverage uniformity greater than 97%, maximizing coverage of all target regions with the minimum total reads. This high coverage uniformity allows you to multiplex more samples on the same sequencing run.

The density plot shows the portion of positions (y-axis) in BRCA1 and BRCA2 with the indicated per-base ratio to median coverage and depicts uniformity based on the removal of PCR duplicates (blue) or not. Data is taken from 250K reads using 12 cycles of the first PCR followed by 20 cycles of the second PCR.

VariantPlex BRCA1/2 Kit coverage uniformity

Mutation Calling

The VariantPlex BRCA1/2 Kit contains primers to detect virtually all known mutation samples including SNP, insertions, and deletions. The table below the gene variants that were accurately called when using mutation-positive samples.

Gene Variant Type
BRCA1 4186C>G_R1443G SNP
BRCA1 185delAG Del
BRCA1 213-11T>G SNP
BRCA1 3875del4_FS1252TER Del
BRCA1 2187delA_K690fsX700 Del
BRCA1 2274insA_C719fsX725 Ins
BRCA1 GLU1250TER SNP
BRCA1 5438insC_N1774fsX Ins
BRCA1 5382insC Ins
BRCA1 1323delG_S401Xfs409 Del
BRCA1 5256delG_V1713X Del
BRCA1 C61G SNP
BRCA1 4184del4_FS1364TER Del
BRCA1 5677insA_Y1853X Ins
BRCA1 916delTT_E266fsX285 Del
BRCA2 353A>G_Y42C SNP
BRCA2 5946delCT_L1908Rfs2X Del
BRCA2 10204A>T_K3326X SNP
BRCA2 983del4_D252fsX275 Del
BRCA2 810G>A_W194X SNP
BRCA2 6174delT_S1982fsX2003 Del
BRCA2 6503delTT_R2092fsX2099 Del
BRCA2 6426delTT_V2066fsX2076 Del

BRCA1 and BRCA2

BRCA1 and BRCA2 are human genes, and the corresponding proteins play an important role maintaining genomic stability by promoting repair of double-strand DNA breaks1. Mutations in BRCA1 or BRCA2 genes can prevent protein translation or result in protein misfunction. DNA repair is thus affected, resulting in genetic alterations that lead in 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” disease (i.e., estrogen and progesterone receptor-negative and with no HER2/nue overexpression)4, resulting in nonresponse to hormonal therapy or targeted therapies against the HER2. While most triple-negative breast cancers are difficult to treat, there is evidence suggesting that prognosis is favorable when linked to BRCA1/2 mutations5.

Breast cancer incidence rates infographic

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. Recently, there has been activity related to drug development for ovarian cancer patients with BRCA1/2 mutations6.

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 cancer7. Men with mutations are at increased risk of male breast cancer and prostate cancer8, and evidence also suggests that both sexes are at increased risk of pancreatic cancer9.


References

  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
    /genetics/brca-fact-sheet
    . 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. 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.
  6. FDA News Release: FDA approves Lynparza to treat advanced ovarian cancer http://www.fda.gov/
    NewsEvents/Newsroom/
    PressAnnouncements/ucm427554.htm
    . Accessed 27 February 2015.
  7. 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.
  8. 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.
  9. 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.

How to contact us

Address

2477 55th Street, Suite 202

Boulder, CO 80301

Phone

Phone: (877) 771 1093

Phone: (303) 357 9001

All content © 2017 ArcherDX, Inc.

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