Hereditary Cancer Panel

Hereditary Cancer Panel, Sequencing and Deletion/Duplication 2012032
Method: Massively Parallel Sequencing/Exonic Oligonucleotide-based CGH Microarray

Indication for testing:

  • Recommended test to confirm a diagnosis of a hereditary cancer syndrome in individuals with personal or family history consistent with features of more than one cancer syndrome.
  • When a relative has a previously identified pathogenic sequence variant, see Familial Mutation, Targeted Sequencing (2001961).
Familial Mutation, Targeted Sequencing 2001961
Method: 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.

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 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

References 

Dome J, Huff V. Wilms Tumor Predisposition. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Oct 2016; Accessed: Nov 2018]

Doros L, Schultz K, Stewart D, Bauer A, Williams G, Rossi C, Carr A, Yang J, Dehner L, Messinger Y, Hill D. DICER1-Related Disorders. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Accessed: Nov 2018]

Else T, Greenberg S, Fishbein L. Hereditary Paraganglioma-Pheochromocytoma Syndromes. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Oct 2018; Accessed: Nov 2018]

Evans D, Farndon P. Nevoid Basal Cell Carcinoma Syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Mar 2018; Accessed: Nov 2018]

Friedman J. Neurofibromatosis 1. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Revision: May 2018; Accessed: Nov 2018]

Greengard E, Park JR. ALK-Related Neuroblastic Tumor Susceptibility. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Apr 2015; Accessed: Nov 2018]

Haidle J, Howe JR. Juvenile Polyposis Syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Mar 2017; Accessed: Nov 2018]

Jasperson K, Patel S, Ahnen D. APC-Associated Polyposis Conditions. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Feb 2017; Accessed: Nov 2018]

Lohmann D, Gallie B. Retinoblastoma. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Nov 2018; Accessed: Nov 2018]

Marquard J, Eng C. Multiple Endocrine Neoplasia Type 2. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Jun 2015; Accessed: Nov 2018]

NCCN Clinical Practice Guidelines in Oncology, Genetic/Familial High-Risk Assessment: Breast and Ovarian, Version 2.2019. National Comprehensive Cancer Network. Fort Washington, PA [Last Updated: Jul 2018; Accessed: Nov 2018]

NCCN Clinical Practice Guidelines in Oncology, Genetic/Familial High-Risk Assessment: Colorectal. Version 1.2018. National Comprehensive Cancer Network. Fort Washington, PA [Updated: Jul 2018; Accessed: Jan 2019]

Nemes K, Bens S, Bourdeaut F, Hasselblatt M, Kool M, Johann P, Kordes U, Schneppenheim R, Siebert R, Fruhwald M. Rhabdoid Tumor Predisposition Syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Accessed: Nov 2018]

Northrup H, Koenig M, Pearson D, Au K. Tuberous Sclerosis Complex. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Jul 2018; Accessed: Nov 2018]

Pilarski R, Rai K, Cebulla C, Abdel-Rahman M. BAP1 Tumor Predisposition Syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Accessed: Nov 2018]

Pithukpakorn M, Toro JR. Hereditary Leiomyomatosis and Renal Cell Cancer. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Aug 2015; Accessed: Nov 2018]

Toro JR. Birt-Hogg-Dubé Syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Aug 2014; Accessed: Nov 2018]

van Leeuwaarde R, Ahman S, Links T, Giles R. Von Hippel-Lindau Syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Sep 2018; Accessed: Nov 2018]

Weese-Mayer D, Marazita M, Rand C, Berry-Kravis E. Congenital Central Hypoventilation Syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews, University of Washington, 1993-2018. Seattle, WA [Last Update: Jan 2014; Accessed: Nov 2018]

Last Update: April 2019