Comprehensive Hereditary Cancer Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: ON1001

The Blueprint Genetics Comprehensive Hereditary Cancer Panel analyzes 117 genes associated with inherited suscebtibility to cancer.

This Panel covers genes associated with a broad spectrum of hereditary cancer syndromes, conferring susceptibility to hematological and/or solid tumors. The Comprehensive Hereditary Cancer Panel is suited for detecting heritable germline mutations and may not be used for the detection of somatic mutations in tumor tissue. This Panel covers all genes included in individual Blueprint Genetics Hereditary Cancer subpanels.

About Hereditary Cancers

Hereditary cancer syndromes account for approximately 5-10% of all cancer. These cancers originate from gastrointestinal tract, endocrine and neuroendocrine systems or from different organs like lung, kidneys, liver, pancreas, skin, and eyes. Hereditary cancer is suspected when there are multiple relatives on the same side of the family with the same or related forms of cancer, cancer at an early age or multiple cancers in an individual. The most common inherited cancer syndromes are hereditary breast and ovarian cancer syndrome, Lynch syndrome (also known as hereditary non-polyposis colorectal cancer), Li-Fraumeni syndrome, Cowden syndrome, familial adenomatous polyposis, Von-Hippel Lindau syndrome, and multiple endocrine neoplasia type 1 and type 2. Most of the hereditary cancer syndromes are inherited in an autosomal dominant manner and penetrance is high. Genetic testing is the most effective way to identify individuals with genetic predisposition of developing cancer. Accurate genetic diagnosis enables personal cancer risk assessment and inherited genetic defect can be taken into account when planning the treatment or moreover the follow-up of both unaffected and affected persons. In most of the cases, cancer mortality can be significantly reduced in high-risk individuals by regular surveillance and preventive strategies.

Availability

Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more.

Genes in the Comprehensive Hereditary Cancer Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
AIPPituitary adenoma, familial isolatedAD54106
ALKNeuroblastomaAD1712
APCGardner syndrome, Desmoid disease, hereditary, Familial adenomatous polyposisAD2941780
ATMBreast cancer, Ataxia-TelangiectasiaAD/AR455853
AXIN2Oligodontia-colorectal cancer syndromeAD615
BAP1Tumor predisposition syndromeAD1373
BARD1Breast cancerAD5453
BLMBloom syndromeAR5392
BMPR1A*Polyposis, juvenile intestinalAD38108
BRCA1*Pancreatic cancer, Breast-ovarian cancer, familialAD22072054
BRCA2Fanconi anemia, Medulloblastoma, Glioma susceptibility, Pancreatic cancer, Wilms tumor, Breast-ovarian cancer, familialAD/AR25141791
BRIP1Fanconi anemia, Breast cancerAD/AR8787
BUB1BMosaic variegated aneuploidy syndrome, Premature chromatid separation traitAD/AR1222
CDC73Carcinoma, parathyroid, Hyperparathyroidism, Hyperparathyroidism-jaw tumor syndromeAD2386
CDH1CDH1-related cancerAD66183
CDK4Melanoma, cutaneous malignantAD211
CDKN1BMultiple endocrine neoplasiaAD923
CDKN1CBeckwith-Wiedemann syndrome, IMAGE syndromeAD2579
CDKN2AMelanoma, familial, Melanoma-pancreatic cancer syndromeAD37217
CEBPAAcute myeloid leukemia, familialAD129
CEP57Mosaic variegated aneuploidy syndromeAR43
CHEK2*Li-Fraumeni syndromeAD/AR93115
CYLDSpiegler-Brooke syndrome, Trichoepithelioma, multiple, CylindromatosisAD34103
DDB2Xeroderma pigmentosumAR415
DICER1*DICER1 syndromeAD96109
DIS3L2*Perlman syndromeAR69
DKC1Hoyeraal-Hreidarsson syndrome, Dyskeratosis congenitaXL4569
EGFRLung cancer, familial, susceptibilty to, Inflammatory skin and bowel disease, neonatal, Acute myeloid leukemia, familialAD/AR1819
ELANENeutropeniaAD30213
EPCAMDiarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposisAD/AR1563
ERCC2Xeroderma pigmentosum, Trichothiodystrophy, photosensitiveAR1890
ERCC3Xeroderma pigmentosum, Trichothiodystrophy, photosensitiveAR916
ERCC4Fanconi anemia, Xeroderma pigmentosumAR1137
ERCC5Xeroderma pigmentosum, Xeroderma pigmentosum/Cockayne syndromeAR1751
EXO1Lynch syndromeAD/AR15
EXT1Multiple cartilagenious exostoses 1AD28479
EXT2Multiple cartilagenious exostoses 2AD20230
EZH2Weaver syndromeAD1436
FANCAFanconi anemiaAR33474
FANCBFanconi anemiaXL714
FANCCFanconi anemiaAR3434
FANCD2*Fanconi anemiaAR1049
FANCEFanconi anemiaAR39
FANCFFanconia anemiaAR68
FANCGFanconi anemiaAR1173
FANCIFanconi anemiaAR827
FANCLFanconi anemiaAR615
FANCMFanconi anemiaAR113
FHHereditary leiomyomatosis and renal cell cancerAD89161
FLCNBirt-Hogg-Dube syndrome, Pneumothorax, primary spontaneousAD85165
GATA2Myelodysplastic syndrome, Chronic neutropenia associated with monocytopenia, evolving to myelodysplasia and acute myeloid leukemia, Acute myeloid leukemia, Emberger syndrome, ImmunodeficiencyAD1976
GPC3Simpson-Golabi-Behmel syndromeXL2265
GREM1Hereditary mixed polyposis syndromeAD/AR8
HNF1AMaturity onset diabetes of the young, Renal cell carcinoma, nonpapillary clear cell, Liver adenomatosisAD47505
HOXB13Familial prostate cancerAD/AR6
HRASCostello syndrome, Congenital myopathy with excess of muscle spindlesAD3026
KITGastrointestinal stromal tumorAD27111
KRAS*Noonan syndrome, Cardiofaciocutaneous syndromeAD4638
MAXPheochromocytomaAD623
MEN1Hyperparathyroidism, familial primary, Multiple endocrine neoplasiaAD124699
METDeafness, Renal cell carcinoma, papillaryAD/AR1323
MITFRenal cell carcinoma with or without malignant melanoma, Tietz albinism-deafness syndrome, Waardenburg syndrome, Melanoma, cutaneous malignantAD1550
MLH1Muir-Torre syndrome, Endometrial cancer, Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR6701084
MLH3Colorectal cancer, hereditary nonpolyposis, Endometrial carcinomaAD425
MRE11AAtaxia-telangiectasia-like disorder-1AD2538
MSH2Muir-Torre syndrome, Endometrial cancer, Colorectal cancer, hereditary nonpolyposis,, Mismatch repair cancer syndromeAD/AR6461089
MSH6Endometrial cancer, Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR308426
MUTYHFamilial adenomatous polyposis,, Colorectal adenomatous polyposis, with pilomatricomasAR69129
NBNBreast cancer, Nijmegen breakage syndromeAD/AR5762
NF1*Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndromeAD2612607
NF2Schwannomatosis, NeurofibromatosisAD24423
NSD1Sotos syndrome, Weaver syndrome, Beckwith-Wiedemann syndromeAD212461
PALB2Fanconi anemia, Pancreatic cancer, Breast cancerAD/AR237223
PHOX2BCentral hypoventilation syndrome, congenital, Neuroblastoma, susceptiblity to, Neuroblastoma with Hirschsprung diseaseAD570
PMS1Hereditary nonpolyposis colon cancerAD/AR111
PMS2*Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR151266
POLD1Colorectal cancerAD117
POLEColorectal cancer, Facial dysmorphism, immunodeficiency, livedo, and short stature syndrome (FILS syndrome)AD/AR123
PPM1DHereditary breast cancerAD49
PRF1Lymphoma, non-Hodgkin, Aplastic anemia, adult-onset, Hemophagocytic lymphohistiocytosisAR15165
PRKAR1AMyxoma, intracardiac, Acrodysostosis, Pigmented nodular adrenocortical disease, Carney complexAD50173
PTCH1Basal cell nevus syndromeAD46348
PTEN*Bannayan-Riley-Ruvalcaba syndrome, Lhermitte-Duclos syndrome, Cowden syndromeAD192564
PTPN11LEOPARD syndrome, Noonan syndrome, MetachondromatosisAD122129
RAD50Breast cancerAD7440
RAD51CFanconi anemia, Breast-ovarian cancer, familialAD/AR4986
RAD51DOvarian cancer, familialAD2550
RB1RetinoblastomaAD1111013
RECQL4Baller-Gerold syndrome, RAPADILINO syndrome, Rothmund-Thomson syndromeAR3492
RETHirschsprung disease, Central hypoventilation syndrome, congenital, Pheochromocytoma, Medullary thyroid carcinoma, Multiple endocrine neoplasiaAD/AR80405
RHBDF2Tylosis with esophageal cancerAD23
RUNX1Platelet disorder, familial, with associated myeloid malignancyAD1374
SBDS*Aplastic anemia, Shwachman-Diamond syndrome, Severe spondylometaphyseal dysplasiaAD/AR1288
SDHA*Leigh syndrome/Mitochondrial respiratory chain complex II deficiency, Gastrointestinal stromal tumor, Paragangliomas, Dilated cardiomyopathy (DCM)AD/AR2339
SDHAF2ParagangliomasAD25
SDHBParaganglioma and gastric stromal sarcoma, Pheochromocytoma, Gastrointestinal stromal tumor, Paragangliomas, Cowden-like syndromeAD72249
SDHCParaganglioma and gastric stromal sarcoma, Gastrointestinal stromal tumor, ParagangliomasAD1453
SDHDParaganglioma and gastric stromal sarcoma, Pheochromocytoma, Paragangliomas, Carcinoid tumors, intestinal, Cowden syndromeAD42158
SLX4Fanconi anemiaAR831
SMAD4Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasiaAD119128
SMARCB1Schwannomatosis, Rhabdoid tumor predisposition syndromeAD17115
STK11Peutz-Jeghers syndromeAD69399
SUFUMedulloblastoma, Basal cell nevus syndromeAD727
TERCAplastic anemia, Pulmonary fibrosis and/or bone marrow failure, telomere-related, Dyskeratosis congenitaAD3660
TERTAplastic anemia, Pulmonary fibrosis and/or bone marrow failure, telomere-related, Dyskeratosis congenitaAD/AR39133
TINF2Revesz syndrome, Dyskeratosis congenitaAD2033
TMEM127PheochromocytomaAD2038
TP53Colorectal cancer, Li-Fraumeni syndrome, Ependymoma, intracranial, Choroid plexus papilloma, Breast cancer, familial, Adrenocortical carcinoma, Osteogenic sarcoma, Hepatoblastoma, Non-Hodgkin lymphomaAD148391
TSC1Lymphangioleiomyomatosis, Tuberous sclerosisAD61306
TSC2Lymphangioleiomyomatosis, Tuberous sclerosisAD141977
VHLErythrocytosis, familial, PheochromocytomaAD/AR143573
WRN*Werner syndromeAR2097
WT1Denys-Drash syndrome, Frasier syndrome, Wilms tumorAD23165
XPAXeroderma pigmentosumAR1047
XPCXeroderma pigmentosumAR1591
XRCC2Hereditary breast cancerAD/AR313
  • * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Blueprint Genetics offers a comprehensive hereditary cancer panel that covers classical genes associated with Beckwith-Wiedemann syndrome, Bloom syndrome, familial adenomatous polyposis, Gorlin syndrome, hereditary breast and ovarian cancer syndrome, hereditary cancer, hereditary nonpolyposis colon cancer, hereditary pheochromocytoma-paraganglioma, hereditary retinoblastoma, juvenile polyposis syndrome, Li-Fraumeni syndrome, medulloblastoma predisposition, multiple endocrine neoplasia, nephroblastoma, neurofibromatosis type 1, neurofibromatosis type 2, Peutz-Jeghers syndrome, pleuropulmonary blastoma family tumor susceptibility syndrome, Rothmund-Thomson syndrome, Simpson-Golabi-Behmel syndrome, tuberous sclerosis complex, Von Hippel-Lindau disease and Werner syndrome. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Please see our latest validation report showing sensitivity and specificity for SNPs and indels, sequencing depth, % of the nucleotides reached at least 15x coverage etc. If the Panel is not present in the report, data will be published when the Panel becomes available for ordering. Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. All the Panels available for ordering have sensitivity and specificity higher than > 0.99 to detect single nucleotide polymorphisms and a high sensitivity for indels ranging 1-19 bp. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile. Detection limit for Del/Dup analysis varies through the genome from one to six exon Del/Dups depending on exon size, sequencing coverage and sequence content.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ81479
DEL/DUP81479

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

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