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Hereditary Breast and Ovarian Cancer BRCA1/2 Sequencing and Deletion/Duplication Panel

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing and Deletion/Duplication Testing via aCGH

Test Code TestIndividual Gene PriceCPT Code Copy CPT Codes
1949 BRCA1 and BRCA2$990.00 81211, 81213 Add to Order
Full Panel Price* $990.00
Pricing Comment

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information. If you would like to order a subset of these genes contact us to discuss pricing.

For Sanger Sequencing click here.
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

The overall prevalence of germline BRCA1 or BRCA2 pathogenic variants in the general population is 1:400 to 1:800, and higher rates depending on the specific ethnicity, such as 1:40 in the Ashkenazi Jewish population. Pathogenic variants will be detected by sequencing in 90% of individuals with an identifiable mutation. Previously, BRCA1 variants were observed in 63% of these cases and BRCA2 variants in 37% of these cases (Petrucelli 2013). BRCA1 mutation carriers tend to have breast tumors that are estrogen receptor (ER) negative, progesterone receptor (PR) negative and basal type tumors, whereas BRCA2 mutation carriers have breast tumors that are ER positive, PR positive, and have a luminal phenotype (Pruthi et al. 2010). Individuals with HBOC with a more severe personal or family history tend to have pathogenic variants in BRCA1 vs. BRCA2 due to higher penetrance of mutations in the BRCA1 gene (Antoniou et al. 2000). Pathogenic variants will be detected by copy number analysis in 10% of individuals with an identifiable germline mutation. Previously, BRCA1 variants were observed in 90% of these cases and BRCA2 variants in 10% of these cases (Petrucelli 2013). Large rearrangements (e.g. deletions, duplications, tripications), including the five most commonly reported BRCA1 alterations (Hendrickson et al. 2005), can be detected using this test. High-risk patients, defined as individuals with early onset (< 50 years of age) invasive or in situ breast cancer or ovarian cancer or male breast cancer, and with 2 or more relatives with HBOC have higher rates of large rearrangements. Specific ethnic populations (i.e. Latin American/Caribbean) have also been shown to have higher rates of copy number alterations (Judkins et al. 2012).

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Clinical Features

Hereditary breast and ovarian cancer (HBOC) syndrome is an inherited disorder that is mainly associated with tumors of the breasts and ovaries. Other malignancies in HBOC families can include melanoma, pancreatic and prostate cancer.  In comparison to sporadic breast and ovarian cancers, HBOC syndrome tumors tend to occur at an earlier age (i.e. < 50 years), to occur bilaterally, to occur in multiple family members, to include males with breast cancer, and to occur with a higher predisposition in specific ethnicities, such as the Ashkenazi Jewish population (Petrucelli et al. 2013; Pruthi et al. 2010). Identifying individuals with a high-risk for developing HBOC may allow for early detection of tumor growth and allow for prophylactic mastectomy and/or oophorectomy or other treatments (Smith 2012).

The majority of breast and ovarian cancers occur sporadically. However, approximately 5-10% of breast, and 10-15% of ovarian cancer cases are due to pathogenic variants in specific genes, particularly BRCA1 and BRCA2, that significantly increase an individual's risk of developing these cancers (Marchina et al. 2010). In addition, HBOC syndrome may also be the result of lower penetrance mutations in other genes, which confer a moderate risk (Berliner et al. 2013).

Genetics

Hereditary breast and ovarian cancer is inherited in an autosomal dominant manner and presents with high, although incomplete, penetrance. Pathogenic variants in a number of genes have been reported to significantly increase an individual’s likelihood for developing breast cancer (Tan et al. 2008). Among those, germline mutations in the most common highly penetrant mutated breast cancer genes, BRCA1 and BRCA2 (Miki et al. 1994; Wooster et al. 1995), appear to provide the highest relative risk with lifetime prevalence up to 40% to 85% for breast cancer (Rebbeck et al. 2009; Pruthi et al. 2010), and 10-46% for ovarian cancer depending on the gene mutated (Smith 2012; Pruthi et al. 2010). Hereditary BRCA1 and BRCA2 variants account for approximately 25-60% of inherited breast cancer (Pruthi et al. 2010; Meindl et al. 2011) and 11-39% for ovarian cancer (Berliner et al. 2013).

BRCA1 is a tumor suppressor that is involved in cellular processes including DNA damage repair, cell cycle progression, gene transcription and ubiquitination. BRCA2 is a tumor suppressor that along with RAD51 has a large role in DNA repair processes and genome stability. Most pathogenic variants of the BRCA1 and BRCA2 genes are private variants which are observed in a single family or in a small number of families. Three pathogenic variants in the BRCA genes are commonly found in Ashkenazi Jewish individuals: c.68_69delAG (BRCA1), c.5266dupC (BRCA1), and c.5946delT (BRCA2), and the coexistence of more than one founder mutation has been reported in some Ashkenazi Jewish families . Most BRCA variants are inherited from a parent who may or may not have been affected with HBOC due to incomplete penetrance of the mutation, gender, and other factors (Petrucelli 2013).  Most pathogenic variants result in predicted truncated BRCA1 or BRCA2 proteins.

Testing Strategy

For this Next Generation (NextGen) panel, the full coding regions plus ~20 bp of non-coding DNA flanking each exon are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

Deletion and duplication testing is analyzed using array comparative genomic hybridization.

Each gene can also be tested individually using our Sanger sequencing assays. Please see our test menu.

Indications for Test

Individuals with a clinical presentation of Hereditary Breast and Ovarian Cancer syndrome or a family history of HBOC. Clinical presentation or family history includes early-onset of breast cancer (i.e. BRCA2 variant than a BRCA1 variant. Prostate cancer rates are elevated in individuals with BRCA1 or BRCA2 variants. Earlier detection of clinical abnormalities may lead to earlier treatment and better outcomes. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

This is a predictive test and it only provides information regarding the likelihood of breast and/or ovarian cancer.  A positive test does not mean that a person will have breast and/or ovarian cancer, and a negative test does not mean that a person will not get breast and/or ovarian cancer.

Gene

Official Gene Symbol OMIM ID
BRCA1 and BRCA2 600185
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Antoniou AC, Gayther SA, Stratton JF, Ponder BA, Easton DF. 2000. Risk models for familial ovarian and breast cancer. Genet. Epidemiol. 18: 173–190. PubMed ID: 10642429
  • Berliner JL, Fay AM, Cummings SA, Burnett B, Tillmanns T. 2012. NSGC Practice Guideline: Risk Assessment and Genetic Counseling for Hereditary Breast and Ovarian Cancer. Journal of Genetic Counseling 22: 155–163. PubMed ID: 23188549
  • Hendrickson BC, Judkins T, Ward BD, Eliason K, Deffenbaugh AE, Burbidge LA, Pyne K, Leclair B, Ward BE, Scholl T. 2005. Prevalence of five previously reported and recurrentBRCA1 genetic rearrangement mutations in 20,000 patients from hereditary breast/ovarian cancer families. Genes, Chromosomes and Cancer 43: 309–313. PubMed ID: 15846789
  • Judkins T, Rosenthal E, Arnell C, Burbidge LA, Geary W, Barrus T, Schoenberger J, Trost J, Wenstrup RJ, Roa BB. 2012. Clinical significance of large rearrangements in BRCA1 and BRCA2. Cancer 118: 5210–5216. PubMed ID: 22544547
  • Marchina E, Fontana MG, Speziani M, Salvi A, Ricca G, Di Lorenzo D, Gervasi M, Caimi L, Barlati S. 2010. BRCA1 and BRCA2 genetic test in high risk patients and families: counselling and management. Oncology Reports 24: 1661-1667. PubMed ID: 21042765
  • Meindl A, Ditsch N, Kast K, Rhiem K, Schmutzler RK. 2011. Hereditary breast and ovarian cancer: new genes, new treatments, new concepts. Dtsch Arztebl Int 108: 323–330. PubMed ID: 21637635
  • Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett LM, Ding W. 1994. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266: 66–71. PubMed ID: 7545954
  • Petrucelli N, Daly MB, Feldman GL. 2013. BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301425
  • Pruthi S, Gostout BS, Lindor NM. 2010. Identification and Management of Women With BRCA Mutations or Hereditary Predisposition for Breast and Ovarian Cancer. Mayo Clinic Proceedings 85: 1111–1120. PubMed ID: 21123638
  • Rebbeck TR, Kauff ND, Domchek SM. 2009. Meta-analysis of Risk Reduction Estimates Associated With Risk-Reducing Salpingo-oophorectomy in BRCA1 or BRCA2 Mutation Carriers. JNCI Journal of the National Cancer Institute 101: 80–87. PubMed ID: 19141781
  • Smith EC. 2012. An Overview of Hereditary Breast and Ovarian Cancer Syndrome. Journal of Midwifery & Women’s Health 57: 577–584. PubMed ID: 23050669
  • Tan DSP, Marchio C, Reis-Filho JS. 2008. Hereditary breast cancer: from molecular pathology to tailored therapies. Journal of Clinical Pathology 61: 1073–1082. PubMed ID: 18682420
  • Wooster R, Bignell G, Lancaster J, Swift S, Seal S, Mangion J, Collins N, Gregory S, Gumbs C, Micklem G. 1995. Identification of the breast cancer susceptibility gene BRCA2. Nature 378: 789–792. PubMed ID: 8524414
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TEST METHODS

NextGen Sequencing and Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

NextGen Sequencing

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Deletion/Duplication Testing via aCGH

As required, DNA is extracted from the patient specimen. Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product.  The combined sample is loaded onto the designed array and hybridized for at least 22 hours at 65ºC.  Arrays are then washed and scanned immediately with 2.5 µM resolution.  Only data for the gene(s) of interest for each patient are extracted and analyzed.

PreventionGenetics’ high density gene-centric (HDGC) aCGH is designed to have comprehensive coverage for both coding and non-coding regions for each targeted gene with very high density probe coverage.  The average probe spacing within each exon is 47 bp or a minimum of three probes per exon covering all targeted exons and UTRs.  The average probe spacing is 289 bp covering all intronic, 2kb upstream and downstream regions of each targeted gene.  In addition, the flanking 300-bp intronic sequence on either side of targeted exons has enriched probe coverage.  Therefore, PreventionGenetics’ aCGH enables the detection of relatively small deletion and amplification mutations within a single exon of a given gene or deletion and amplification mutations encompassing the entire gene.

Analytical Validity

NextGen Sequencing

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable. 

Deletion/Duplication Testing via aCGH

PreventionGenetics’ high density gene-centric custom designed aCGH enables the detection of relatively small deletion and amplification mutations (down to ~300 bp) within a single exon of a given gene or deletion and amplification mutations encompassing the entire gene. PreventionGenetics has established and verified this test’s accuracy and precision.

Analytical Limitations

NextGen Sequencing

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most cases, we are unable to determine the phase of sequence variants.  In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants due to somatic mosaicism is limited.  Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Deletion/Duplication Testing via aCGH

Any copy number changes smaller than 300bps (within the targeted region) may not be detected by our array.

This array may not detect deletion and amplification mutations present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype

Breakpoints, if happened outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory

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Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • The first four pages of the requisition form must accompany all specimens.
  • Billing information is on the third and fourth pages.
  • Specimen and shipping instructions are listed on the fifth and sixth pages.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3-5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10-20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is good for up to 48 hours.
  • If refrigerated, blood specimen is good for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • NextGen Sequencing Tests: Send in screw cap tube at least 10 µg of purified DNA at a concentration of at least 50 µg/ml
  • Sanger Sequencing Tests: Send in a screw cap tube at least 15 µg of purified DNA at a concentration of at least 20 µg/ml. For tests involving the sequencing of more than three genes, send an additional 5 µg DNA per gene. DNA may be shipped at room temperature.
  • Deletion/Duplication via aCGH: Send in screw cap tube at least 1 µg of purified DNA at a concentration of at least 100 µg/ml.
  • Whole-Genome Chromosomal Microarray: Collect at least 5 µg of DNA in TE (10 mM Tris-cl pH 8.0, 1mM EDTA), dissolved in 200 µl at a concentration of at least 100 ng/ul (indicate concentration on tube label). DNA extracted using a column-based method (Qiagen) or bead-based technology is preferred.

CELL CULTURE

(Delivery accepted Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Ship at least two T25 flasks of confluent cells.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We do not culture cells.