FeedbackMassively Parallel Sequencing/Exonic Oligonucleotide-based CGH Microarray
Polymerase Chain Reaction/Sequencing
Indication for testing:
- Recommended test if there is a known familial sequence variant previously identified in a family member.
- A copy of the family member’s test result documenting the familial variant is required.
See Related Tests
Pathogenic variants in the genes analyzed by this panel cause variable phenotypes and cancer risks, and have been implicated in hereditary cancer. Hereditary predisposition is often characterized by early age of cancer onset (typically before age 50), and the development of two or more cancers, multifocal cancers, or similar cancers in an individual or in a closely related family member(s). See Genes Tested table below for more details regarding the genes and syndromes included on the Hereditary Cancer Panel.
Disease Overview
Etiology
Approximately 5-10% of cancer is associated with a hereditary cause.
Inheritance
- All genes tested on this panel are autosomal dominant with the exception of:
- SDHD gene – autosomal dominant with paternal parent-of-origin effect
- MAX and SDHAF2 genes – autosomal dominant with possible paternal parent-of-origin effect
- MUTYH gene – autosomal recessive but may also have autosomal dominant risks that are not well-defined
- MSH3 and NTHL1 – autosomal recessive
- Some genes are associated with autosomal recessive childhood cancer predisposition or other syndromes.
- See table below for additional details.
Test Description
See Genes Tested table for genes included in the panel.
Clinical Sensitivity
Variable, dependent on phenotype/condition
Testing Strategy
- Indications for ordering
- To diagnose a hereditary cancer syndrome in an individual with a personal and/or family history consistent with more than one cancer syndrome
- Contraindications for ordering
- Should not be ordered to detect somatic variants associated with malignancy because sensitivity for mosaic variants is low with methodology used for germline assays
- Individuals with hematological malignancy and/or a previous allogenic bone marrow transplant should not undergo molecular genetic testing on peripheral blood specimen.
- Testing of cultured fibroblasts is required for accurate interpretation of test results.
- When a relative has a previously identified pathogenic variant, see Familial Mutation, Targeted Sequencing (2001961).
Limitations
- A negative result does not exclude a heritable form of cancer.
- Diagnostic errors can occur due to rare sequence variations.
- Interpretation of this test result may be impacted if this individual has had an allogeneic stem cell transplantation.
- The following will not be evaluated:
- Variants outside the coding regions and intron-exon boundaries of the targeted genes
- Regulatory region variants and deep intronic variants
- Breakpoints of large deletions/duplications
- Deletions/duplications in AXIN2, MSH3, NF1, RECQL, SMARCA4, WT1
- Sequence variants in EPCAM
- Noncoding transcripts
- The following exons are not sequenced due to technical limitations of the assay:
- CHEK2 (NM_001349956) 4; (NM_001005735) 3; (NM_007194) 10, 12, 13, 14, 15
- RECQL (NM_002907) 14, 15
- SDHC (NM_001035511) 5
- SDHD (NM_001276506) 4
- The following may not be detected:
- Deletions/duplications/insertions of any size by massively parallel sequencing
- Deletions/duplications less than 1kb in the targeted genes
- Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
- Low-level somatic variants
- Single exon deletions/duplications in the following exons:
-
Gene Exon(s) APC
(NM_001127511) 1
BAP1
(NM_004656) 1
BARD1
(NM_000465) 1
BMPR1A
(NM_004329) 9
BRCA1
(NM_007300) 13
CDH1
(NM_004360) 1
CDKN2A
(NM_000077) 2
CDKN2A
(NM_058195) 2
CHEK2
(NM_001005735) 3
CHEK2
(NM_007194) 11, 12, 14, 15
FH
(NM_000143) 1
FLCN
(NM_144997) 8
MAX
(NM_001320415) 5
MAX
(NM_145113) 5
MRE11
(NM_005591) 2
MSH2
(NM_000251) 1
MSH2
(NM_001258281) 2
MSH6
(NM_000179) 10
MUTYH
(NM_001128425) 1
NF2
(NM_000268) 7, 13, 16
NTHL1
(NM_002528) 3, 4, 5, 6
PALB2
(NM_024675) 1
POLD1
(NM_002691) 6, 18, 25
PTEN
(NM_000314) 8, 9
PTEN
(NM_001304717) 1
RAD51D
(NM_002878) 1
RB1
(NM_000321) 1
RET
(NM_020975) 1
SDHD
(NM_001276506) 4
SMARCB1
(NM_003073) 5
SUFU
(NM_001178133) 11
SUFU
(NM_016169) 1
TP53
(NM_001126113) 10
TP53
(NM_001126114) 10
TSC2
(NM_000548) 17, 29, 41
VHL
(NM_000551) 1
Analytical Sensitivity
- For Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) of PMS2: 99%
- For massively parallel sequencing:
| Variant Class | Analytical Sensitivity (PPA) Estimatea (%) | Analytical Sensitivity (PPA) 95% Credibility Regiona (%) |
|---|---|---|
|
SNVs |
99.2 |
96.9-99.4 |
|
Deletions 1-10 bp |
93.8 |
84.3-98.2 |
|
Deletions 11-44 bp |
100 |
87.8-100 |
|
Insertions 1-10 bp |
94.8 |
86.8-98.5 |
|
Insertions 11-23 bp |
100 |
62.1-100 |
|
aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. bp, base pairs; PPA, positive percent agreement; SNVs, single nucleotide variants |
||
Genes Tested
| Gene | MIM Number | Disorder/Associated Cancer(s)/Tumor(s) | Inheritance |
|---|---|---|---|
|
ALK |
105590 |
Associated cancer(s)/tumor(s): neuroblastoma, ganglioneuroblastoma, ganglioneuroma |
AD |
|
APC |
611731 |
Familial adenomatous polyposis (FAP) Attenuated FAP (AFAP) Associated cancer(s)/tumor(s): colon, duodenal, thyroid, pancreas, stomach, medulloblastoma, hepatoblastoma |
AD |
|
ATM |
607585 |
Associated cancer(s)/tumor(s): breast, ovarian, a colorectal a |
AD |
|
Ataxia-telangiectasia (AT) |
AR |
||
|
ATR |
601215 |
Familial cutaneous telangiectasia and cancer syndrome (FCTCS) Associated cancer(s)/tumor(s): oropharyngeal |
AD |
|
Seckel syndrome 1 |
AR |
||
|
AXIN2 |
604025 |
Oligodontia-colorectal cancer syndrome (OSCRCS) Associated cancer(s): colon a |
AD |
|
BAP1 |
603089 |
BAP1 tumor predisposition syndrome (BAP1-TPDS) Associated cancer(s)/tumor(s): uveal melanoma, malignant mesothelioma, cutaneous melanoma, renal cell carcinoma, basal cell carcinoma |
AD |
|
BARD1 |
601593 |
Associated cancer(s)/tumor(s): breast a |
AD |
|
BMPR1A |
601299 |
Juvenile polyposis syndrome (JPS) Associated cancer(s)/tumor(s): colon, stomach, small intestine, pancreas |
AD |
|
BRCA1 |
113705 |
Hereditary breast and ovarian cancer (HBOC) syndrome Associated cancer(s)/tumor(s): breast, ovarian, prostate, pancreas, melanoma |
AD |
|
Fanconi anemia, complementation group S |
AR |
||
|
BRCA2 |
600185 |
Hereditary breast and ovarian cancer (HBOC) syndrome Associated cancer(s)/tumor(s): breast, ovarian, prostate, pancreas, melanoma |
AD |
|
Fanconi anemia, complementation group D1 |
AR |
||
|
BRIP1 |
605882 |
Associated cancer(s)/tumor(s): ovarian, breast a |
AD |
|
Fanconi anemia, complementation group J |
AR |
||
|
CDH1 |
192090 |
Hereditary diffuse gastric cancer (HDGC) Associated cancer(s)/tumor(s): diffuse gastric, lobular breast |
AD |
|
CDK4 |
123829 |
Associated cancer(s)/tumor(s): cutaneous melanoma |
AD |
|
CDKN1B |
600778 |
Multiple endocrine neoplasia (MEN) Type 4 Associated cancer(s)/tumor(s): parathyroid, pituitary, gastrinoma, insulinoma, gastro-entero-pancreatic (GEP), carcinoid, adrenocortical, nonendocrine |
AD |
|
CDKN2A |
600160 |
Familial atypical multiple mole melanoma-pancreatic carcinoma (FAMMM-PC) syndrome (also known as melanoma-pancreatic cancer syndrome) Associated cancer(s)/tumor(s): cutaneous melaoma, pancreas |
AD |
|
CHEK2 |
604373 |
Associated cancer(s)/tumor(s): breast, colorectal, a prostate, a thyroid a |
AD |
|
DICER1 |
606241 |
DICER1-related disorders Associated cancer(s)/tumor(s): pleuropulmonary blastoma, ovarian sex cord-stromal tumors, cystic nephroma, thyroid |
AD |
|
EPCAM |
185535 |
Lynch syndrome/hereditary nonpolyposis colorectal cancer (HNPCC) Associated cancer(s)/tumor(s): colorectal, endometrial, stomach, ovarian, and others |
AD |
|
FH |
136850 |
Hereditary leiomyomatosis and renal cell cancer (HLRCC) Associated cancer(s)/tumor(s): papillary type 2 renal cancer, cutaneous and uterine leiomyomata |
AD |
|
Fumarase deficiency |
AR |
||
|
FLCN |
607273 |
Birt-Hogg-Dube syndrome (BHDS) Associated cancer(s)/tumor(s): renal |
AD |
|
MAX |
154950 |
Associated cancer(s)/tumor(s): pheochromocytoma, paraganglioma |
ADb |
|
MEN1 |
613733 |
Multiple endocrine neoplasia (MEN) type 1 Associated cancer(s)/tumor(s): parathyroid, pituitary, gastrinoma, insulinoma, carcinoid, adrenocorticol |
AD |
|
MET |
164860 |
Hereditary papillary renal cell carcinoma (HPRCC) Associated cancer(s)/tumor(s): papillary type 1 renal cancer |
AD |
|
MLH1 |
120436 |
Lynch syndrome/hereditary nonpolyposis colorectal cancer (HNPCC) Associated cancer(s)/tumor(s): colorectal, endometrial, stomach, ovarian, and others |
AD |
|
Constitutional mismatch repair deficiency (CMMRD) |
AR |
||
|
MRE11/MRE11A |
600814 |
Associated cancer(s)/tumor(s): breast a |
AD |
|
Ataxia-telangiectasia-like disorder |
AR |
||
|
MSH2 |
609309 |
Lynch syndrome/hereditary nonpolyposis colorectal cancer (HNPCC) Associated cancer(s)/tumor(s): colorectal, endometrial, stomach, ovarian, and others |
AD |
|
Constitutional mismatch repair deficiency (CMMRD) |
AR |
||
|
MSH3 |
600887 |
Associated cancer(s)/tumor(s): polyposis, colorectal a |
AR |
|
MSH6 |
600678 |
Lynch syndrome/hereditary nonpolyposis colorectal cancer (HNPCC) Associated cancer(s)/tumor(s): colorectal, endometrial, stomach, ovarian, and others |
AD |
|
Constitutional mismatch repair deficiency (CMMRD) |
AR |
||
|
MUTYH |
604933 |
Associated cancer(s)/tumor(s): breast a |
AD |
|
MUTYH-Associated Polyposis (MAP) Associated cancer(s)/tumor(s): colon, duodenal |
AR |
||
|
NBN |
602667 |
Associated cancer(s)/tumor(s): breast |
AD |
|
Nijmegan Breakage syndrome (NBS) |
AR |
||
|
NF1 |
613113 |
Neurofibromatosis type 1 (NF1) Associated cancer(s)/tumor(s): breast, neurofibromas, gliomas, malignant peripheral nerve sheath tumors, gastrointestinal stromal tumor (GIST), leukemia |
AD |
|
NF2 |
607379 |
Neurofibromatosis type 2 (NF2) Associated cancer(s)/tumor(s): schwannoma, meningioma |
AD |
|
NTHL1 |
602656 |
Associated cancer(s)/tumor(s): polyposis, colorectal a |
AR |
|
PALB2 |
610355 |
Associated cancer(s)/tumor(s): breast, pancreatic a |
AD |
|
Fanconi Anemia, complementation group N |
AR |
||
|
PHOX2B |
603851 |
Congenital central hypoventilation syndrome (CCHS) Associated cancer(s)/tumor(s): neuroblastoma, ganglioneuroblastoma, ganglioneuroma |
AD |
|
PMS2 |
600259 |
Lynch syndrome/hereditary nonpolyposis colorectal cancer (HNPCC) Associated cancer(s)/tumor(s): colorectal, endometrial, stomach, ovarian, and others |
AD |
|
Constitutional mismatch repair deficiency (CMMRD) |
AR |
||
|
POLD1 |
174761 |
Associated cancer(s)/tumor(s): polyposis, colorectal a |
AD |
|
POLE |
174762 |
Associated cancer(s)/tumor(s): polyposis, colorectal a |
AD |
|
PTEN |
601728 |
Cowden syndrome/PTEN hamartoma tumor syndrome Associated cancer(s)/tumor(s): breast, endometrial, thyroid, colon, renal cell carcinoma |
AD |
|
RAD51C |
602774 |
Associated cancer(s)/tumor(s): ovarian |
AD |
|
Fanconi anemia, complementation group O |
AR |
||
|
RAD51D |
602954 |
Associated cancer(s)/tumor(s): ovarian |
AD |
|
RB1 |
614041 |
Retinoblastoma Associated cancer(s)/tumor(s): retinoblastoma, retinoma, pinealoblastoma, osteosarcoma, soft tissue sarcoma, melanoma |
AD |
|
RECQL |
600537 |
Associated cancer(s)/tumor(s): breast a |
AD |
|
RET |
164761 |
Multiple endocrine neoplasia type 2 (MEN2) Associated cancer(s)/tumor(s): medullary thyroid carcinoma, pheochromocytoma, parathyroid adenoma |
AD |
|
SDHAF2 |
613019 |
Associated cancer(s)/tumor(s): paraganglioma |
AD b |
|
SDHB |
185470 |
Associated cancer(s)/tumor(s): paraganglioma, pheochromocytoma, GIST, pulmonary chondroma, renal clear cell carcinoma |
AD |
|
SDHC |
602413 |
Associated cancer(s)/tumor(s): paraganglioma, pheochromocytoma, GIST, pulmonary chondroma, renal clear cell carcinoma |
AD |
|
SDHD |
602690 |
Associated cancer(s)/tumor(s): paraganglioma, pheochromocytoma, GIST, pulmonary chondroma, renal clear cell carcinoma |
ADc |
|
SMAD4 |
600993 |
Juvenile polyposis syndrome (JPS); hereditary hemorrhagic telangiectasia (HHT) syndrome Associated cancer(s)/tumor(s): colon, stomach, small intestine, pancreas |
AD |
|
SMARCA4 |
603254 |
Rhabdoid tumor predisposition syndrome Associated cancer(s)/tumor(s): rhabdoid tumor |
AD |
|
SMARCB1 |
601607 |
Rhabdoid tumor predisposition syndrome Associated cancer(s)/tumor(s): rhabdoid tumor |
AD |
|
STK11 |
602216 |
Peutz-Jeghers syndrome (PJS) Associated cancer(s)/tumor(s): breast, colon, stomach, small intestine, pancreas, ovary, testes, lung |
AD |
|
SUFU |
607035 |
Nevoid basal cell carcinoma syndrome (NBCCS) Associated cancer(s)/tumor(s): basal cell carcinoma, medulloblastoma, fibroma, rhabdomyoma |
AD |
|
TMEM127 |
613403 |
Associated cancer(s)/tumor(s): pheochromocytoma, paraganglioma, GIST, pulmonary chondroma, renal clear cell carcinoma |
AD |
|
TP53 |
191170 |
Li-Fraumeni syndrome (LFS) Associated cancer(s)/tumor(s): soft tissue sarcoma, osteosarcoma, central nervous system (CNS) tumor, breast, adrenocortical carcinoma, choroid plexus carcinoma, rhabdomyosarcoma |
AD |
|
TSC1 |
605284 |
Tuberous sclerosis complex (TSC) Associated cancer(s)/tumor(s): cardiac rhabdomyoma, retinal and other hamartomas, renal angiomyolipoma, subependymal giant cell astrocytoma (SEGA), fibromas |
AD |
|
TSC2 |
191092 |
Tuberous sclerosis complex (TSC) Associated cancer(s)/tumor(s): cardiac rhabdomyoma, retinal and other hamartomas, renal angiomyolipoma, subependymal giant cell astrocytoma (SEGA), fibromas |
AD |
|
VHL |
608537 |
Von Hippel-Lindau (VHL) syndrome Associated cancer(s)/tumor(s): hemangioblasoma, retinal angioma, renal cell carcinoma, pheochromocytoma, neuroendocrine tumors, endolymphatic sac tumors, epididymal and broad ligament cystadenomas |
AD |
|
WT1 |
607102 |
WT1-related Wilms tumor WAGR syndrome Denys-Drash syndrome (DDS) Frasier syndrome Associated cancer(s)/tumor(s): Wilms tumor |
AD |
|
aAssociation is suggested but not well-established at this time bPossible paternal parent-of-origin effect cPaternal parent-of-origin effect AD, autosomal dominant; AR, autosomal recessive |
|||
GeneReviews - Wilms Tumor Predisposition
Dome JS, Huff V. Wilms tumor predisposition. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Oct 2016; Accessed: Feb 2020]
GeneReviews - DICER1-Related Disorders
Doros L, Schultz KA, Stewart DR, et al. DICER1-related disorders. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last update: Apr 2020; Accessed: Jun 2020]
GeneReviews - Hereditary Paraganglioma-Pheochromocytoma Syndromes
Else T, Greenberg S, Fishbein L. Hereditary Paraganglioma-Pheochromocytoma Syndromes. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Oct 2018; Accessed: Feb 2020]
GeneReviews - Multiple Endocrine Neoplasia Type 2
Eng C. Multiple endocrine neoplasia type 2. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Aug 2019; Accessed: Feb 2020]
GeneReviews - Nevoid Basal Cell Carcinoma Syndrome
Evans DG, Farndon PA. Nevoid Basal Cell Carcinoma Syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020.
GeneReviews - Neurofibromatosis 1
Friedman JM. Neurofibromatosis 1. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews, University of Washington; 1993-2020. [Last revision: Jun 2019; Accessed: Jun 2020]
GeneReviews - ALK-Related Neuroblastic Tumor Susceptibility
Greengard EG, Park JR. ALK-Related Neuroblastic Tumor Susceptibility. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Jan 2019; Accessed: Feb 2020]
GeneReviews - APC-Associated Polyposis Conditions
Jasperson KW, Patel SG, Ahnen DJ. APC-associated polyposis conditions. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Feb 2017; Accessed: Feb 2020]
GeneReviews - Juvenile Polyposis Syndrome
Larsen Haidle J, Howe JR. Juvenile polyposis syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews, University of Washington; 1993-2020. [Last update: Mar 2017; Accessed: Oct 2020]
GeneReviews - Retinoblastoma
Lohmann DR, Gallie BL. Retinoblastoma. n: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Nov 2018; Accessed: Feb 2020]
NCCN - Genetic/Familial high-risk assessment: Breast and Ovarian v2.2019
NCCN Clinical Practice Guidelines in Oncology, Genetic/Familial High-Risk Assessment: Breast and Ovarian, Version 2.2019. National Comprehensive Cancer Network. Jul 2018; [Last Updated: Jul 2018; Accessed: Nov 2018]
NCCN - Genetic/Familial High-Risk Assessment: Colorectal v1.2018
NCCN Clinical Practice Guidelines in Oncology, Genetic/Familial High-Risk Assessment: Colorectal. Version 1.2018. National Comprehensive Cancer Network. [Updated: Jul 2018; Accessed: Jan 2019]
GeneReviews - Rhabdoid Tumor Predisposition Syndrome
Nemes K, Bens S, Bourdeaut F, et al. Rhabdoid tumor predisposition syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Initial Posting: Dec 2017; Accessed: Feb 2020]
GeneReviews - Tuberous Sclerosis Complex
Northrup H, Koenig MK, Pearson DA, et al. Tuberous sclerosis complex. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Revision: Apr 2020; Accessed: Jun 2020]
GeneReviews - BAP1 Tumor Predisposition Syndrome
Pilarski R, Rai K, Cebulla C, et al. BAP1 tumor predisposition syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Initial Posting: Oct 2016; Accessed: Feb 2020]
GeneReviews - FH tumor predisposition syndrome
Kamihara J, Schultz KA, Rana HQ. FH tumor predisposition syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last update: Apr 2020; Accessed: Jul 2020]
GeneReviews - Birt-Hogg-Dubé Syndrome
Sattler EC, Steinlein OK. Birt-Hogg-Dubé syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Jan 2020; Accessed: Feb 2020]
GeneReviews - Von Hippel-Lindau Syndrome
van Leeuwaarde RS, Ahmad S, Links TP, et al. Von Hippel-Lindau syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews, University of Washington; 1993-2020. [Last Update: Sep 2018; Accessed: Apr 2020]
GeneReviews - Congenital Central Hypoventilation Syndrome
Weese-Mayer DE, Marazita ML, Rand CM, et al. Congenital Central Hypoventilation Syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2020. [Last Update: Jan 2014; Accessed: Feb 2020]
Indication for testing: