Cancer Sequencing and Deletion/Duplication Panel
- Summary and Pricing
- Clinical Features and Genetics
Sequencing and Deletion/Duplication Testing via aCGH
|Test Code||Test||CPT Code Copy CPT Codes|
|Full Panel Price*||$1390.00|
|Test Code||Test||Total Price||CPT Codes Copy CPT Codes|
|1355||Genes x (35)||$1390.00||81201, 81203, 81214, 81216, 81292, 81294, 81295, 81297, 81298, 81300, 81317, 81319, 81321, 81323, 81403(x3), 81404(x3), 81405(x5), 81406(x4), 81408(x2), 81479(x38)||Add|
NF1 is analyzed by Multiplex Ligation-dependent Probe Amplification. If you would like to order a subset of these genes contact us to discuss pricing.
For ordering targeted known variants, please proceed to our Targeted Variants landing page.
The great majority of tests are completed within 28 days.
Genes tested in this panel have been implicated in hereditary cancer and although individually these genes may be involved in a minority of cancers, the combination of highly, moderately and mildly penetrant pathogenic variants may be responsible for a significant portion of these hereditary cancers. See "Related Tests" section for a full description of each individual disorder.
Clinical sensitivity of the tested genes is given based on each syndrome. Deletion and duplication analysis is not available for BAP1, BUB1B, and MET genes. For CHEK2, only exons 8-10 will be analyzed, which includes all known deletions. Gross deletions/duplications have been reported in up to 12% of APC mutation positive patient samples (Jasperson and Burt 2011). Approximately 1-2% of Ataxia Telangiectasia patients have large genomic deletions involving the ATM gene that can be detected using aCGH (Gatti 2010). Gross deletions of multiple exons in the BLM gene account for approximately 5% of Bloom Syndrome (German et al. 2007). This test is predicted to identify a BMPR1A mutation in 1-2% and a SMAD4 mutation in 2-9% of patients diagnosed with JPS (Haidle and Howe 2011). Pathogenic variants will be detected by copy number analysis in 10% of HBOC 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 ( Large deletions that usually cannot be detected via sequencing have been detected in the CDH1 gene in up to 4% of patients (Kaurah and Huntsman 2011). Clinical sensitivity is not known for KIT mutations in GIST; however gross deletions have been reported for Piebaldism (Ezoe et al. 1995). Gross deletions of the MEN1 gene have been detected in up to 4% of patients (Giusti et al. 2012). Lynch syndrome is attributed to deletions in the MLH1, MSH2, MSH6, and PMS2 genes in approximately 5%, 20%, 7% and 20% of cases, respectively (Kohlmann and Gruber 2012). EPCAM deletions account for 1-3% of Lynch syndrome cases (Kohlmann and Gruber 2012). Deletions in the NF1 gene have been detected in 5% of individuals with Neurofibromatosis Type 1 (Friedman 2012). This test is predicted to detect causative PTEN mutations in ~11% of patients with BRRS but not known for other PTEN related disorders (Eng 2003). Approximately 45% of patients with a positive family history or 21% of patients with no family history of Peutz-Jeghers syndrome will have a pathogenic variant in STK11 by deletion analysis (McGarrity et al. 2013). Deletions in the TP53 gene have been detected in 1% of Li-Fraumeni cases (Schneider et al. 2013). Up to 28% of VHL causative mutations involve gross deletions (Frantzen et al. 1993). The clinical sensitivity of large deletions and duplications for the BRIP1, CDK4, CDKN2A, DICER1, MUTYH, NBN, PALB2, PPM1D, RAD51C, RAD51D and WT1 genes is not known but large duplications/deletions have been reported for most of these genes (Human Mutation Database).
Hereditary cancer syndromes have been observed in approximately 5-10% of diagnosed cancers (Mauer et al. 2013). Hereditary cancers tend to occur at an earlier age (i.e. < 50 years), tumors often occur bilaterally and/or are multifocal, consist of multiple affected family members, may include a less frequent affected gender (i.e. breast cancer in males), can be associated with other clinical features, and occur with a higher predisposition in specific ethnicities, such as the Ashkenazi Jewish population (Lindor et al. 2008). The results of analyzing a group of hereditary cancers can be important for counseling and treatment (O’Daniel and Lee 2012; Imyanitov and Byrski 2013). Additionally, assessment of multiple genes associated with hereditary cancers can be useful in determining personal or familial risks (Foulkes 2008).
This NextGen test analyzes multiple genes involved in multiple hereditary cancer syndromes which are inherited in an autosomal dominant manner. Several types of cancers may be found in a pedigree and this test may help in the differential diagnosis and rule out particular syndromes by simultaneously analyzing multiple genes involved in hereditary cancers.
Breast & Ovarian Cancer - ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MEN1, NBN, PALB2, PPM1D, PTEN, RAD51C, RAD51D, STK11, TP53
DICER1 Syndrome - DICER1
Gastrointestinal Cancers - APC, ATM, BLM, BMPR1A, BUB1B, CDH1, CHEK2, EPCAM, KIT, MLH1, MSH2, MSH6, MUTYH, PMS2, PTEN, SMAD4, STK11, TP53
Li-Fraumeni Syndrome - TP53
Melanoma Predisposition - BAP1, CDK4, CDKN2A
Pancreatic Cancer - APC, ATM, BRCA1, BRCA2, CDKN2A, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, TP53
Renal Cancer - MET, VHL, WT1
Pathogenic variants in the exon 1B promoter of APC have also been associated with gastric adenocarcinoma and proximal polyposis of the stomach (Li et al. 2016).
See individual gene test descriptions for information on clinical features and molecular biology of gene products.
The Cancer NextGen Sequencing Panel analyzes 35 genes that have been associated with hereditary cancers. For this NGS panel, the full coding regions, plus ~20bp 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 method, 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, including the exon 1B promoter region of APC. All pathogenic, undocumented and questionable variant calls are confirmed by Sanger sequencing.
Due to known PMS2 pseudogenes, the PMS2 gene is also analyzed via Sanger sequencing using a long-range PCR strategy.
Please note that for deletion/duplication testing, NF1 is analyzed by Multiplex Ligation-dependent Probe Amplification.
Each gene/group of genes can also be tested using our Sanger sequencing and Deletion/Duplication assays. Please see our test menu.
Indications for Test
Individuals with a clinical presentation of a cancer syndrome or a family history of cancer. Clinical presentation or family history includes early-onset cancer (i.e. multiple primary cancers, multiple family members with cancer, and individuals with an Ashkenazi descent with a concern for cancer. 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.
|Official Gene Symbol||OMIM ID|
- Genetic Counselor Team - firstname.lastname@example.org
- Jerry Machado, PhD, DABMG, FCCMG - email@example.com
- Eng C. 2003. PTEN: One Gene, Many Syndromes. Human Mutation 22: 183–198. PubMed ID: 12938083
- Ezoe K, Holmes SA, Ho L, Bennett CP, Bolognia JL, Brueton L, Burn J, Falabella R, Gatto EM, Ishii N. 1995. Novel mutations and deletions of the KIT (steel factor receptor) gene in human piebaldism. American journal of human genetics 56: 58-66. PubMed ID: 7529964
- Foulkes WD. 2008. Inherited susceptibility to common cancers. New England Journal of Medicine 359: 2143–2153. PubMed ID: 19005198
- Frantzen C, Links TP, Giles RH. 1993. Von Hippel-Lindau Disease. 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: 20301636
- Friedman J. 2012. Neurofibromatosis 1. 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: 20301288
- Gatti R. 2010. Ataxia-Telangiectasia. 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: 20301790
- German J, Sanz MM, Ciocci S, Ye TZ, Ellis NA. 2007. Syndrome-causing mutations of the BLM gene in persons in the Bloom’s Syndrome Registry. Human Mutation 28: 743–753. PubMed ID: 17407155
- Giusti F, Marini F, Brandi ML. 2012. Multiple Endocrine Neoplasia Type 1. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301710
- Human Gene Mutation Database (Bio-base).
- Imyanitov EN, Byrski T. 2013. Systemic treatment for hereditary cancers: a 2012 update. Hereditary Cancer in Clinical Practice 11: 2. PubMed ID: 23548133
- Jasperson KW, Burt RW. 2011. APC-Associated Polyposis Conditions. 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: 20301519
- 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
- Kaurah P, Huntsman DG. 2011. Hereditary Diffuse Gastric 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: 20301318
- Kohlmann W, Gruber SB. 2012. Lynch Syndrome. 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: 20301390
- Larsen Haidle J, Howe JR. 2011. Juvenile Polyposis Syndrome. 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: 20301642
- Li J. et al. 2016. American Journal of Human Genetics. 98: 830-42. PubMed ID: 27087319
- Lindor NM, McMaster ML, Lindor CJ, Greene MH. 2008. Concise Handbook of Familial Cancer Susceptibility Syndromes - Second Edition. JNCI Monographs 2008: 3–93. PubMed ID: 18559331
- Mauer CB, Pirzadeh-Miller SM, Robinson LD, Euhus DM. 2013. The integration of next-generation sequencing panels in the clinical cancer genetics practice: an institutional experience. Genetics in Medicine. PubMed ID: 24113346
- McGarrity TJ, Amos CI, Frazier ML, Wei C. 2013. Peutz-Jeghers Syndrome. 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: 20301443
- O’Daniel JM, Lee K. 2012. Whole-genome and whole-exome sequencing in hereditary cancer: impact on genetic testing and counseling. The Cancer Journal 18: 287–292. PubMed ID: 22846728
- Schneider K, Zelley K, Nichols KE, Garber J. 2013. Li-Fraumeni Syndrome. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301488
NextGen Sequencing and Deletion/Duplication Testing Via Array Comparative Genomic Hybridization
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.
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.
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
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.
- 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.
(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.
(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.
(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.