Hereditary Central Nervous System Cancer Panel, Sequencing and Deletion/Duplication

Last Literature Review: December 2022 Last Update:

To compare directly to other hereditary cancer panels offered by ARUP Laboratories, see the ARUP Hereditary Cancer Panel Comparison table.

  • Recommended test to confirm a hereditary cause of CNS cancer in individuals with a personal or family history of CNS cancer
  • Testing minors for adult-onset conditions is not recommended; testing will not be performed in minors without prior approval.
  • For additional information, please contact an ARUP genetic counselor at 800-242-2787 ext. 2141.

If a familial sequence variant has been previously identified, targeted sequencing for that variant may be appropriate; refer to the Laboratory Test Directory for additional information.

Pathogenic germline variants in multiple genes have been implicated in hereditary central nervous system (CNS) tumors and cancer. Hereditary cancer predisposition is often characterized by early age of onset (typically before age 50), the presence of any number of CNS tumors in a single individual or closely related family member(s), and variable systemic manifestations. See the Genes Tested table for more details regarding the genes included on this test and associated cancers and syndromes.

Genetics

Genes

Refer to the Genes Tested table for genes included in the panel.

Etiology

Approximately 5% of CNS tumors are associated with a hereditary cause.

Inheritance

  • Autosomal dominant
  • Some genes are also associated with autosomal recessive childhood cancer predisposition or other syndromes.

Test Interpretation

Contraindications for Ordering

  • For individuals with a suspected diagnosis of Lynch syndrome, consider testing specific to Lynch syndrome as some relevant variants are not included on this panel. Refer to Lynch Syndrome - Hereditary Nonpolyposis Colorectal Cancer (HNPCC) for more information.
  • 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 allogeneic 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.

Methodology

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
  • Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.
  • Long-range polymerase chain reaction (PCR) followed by nested Sanger sequencing is performed on the following gene and exons:
    • PMS2 (NM_000535) 11, 12, 13, 14, 15
  • Bidirectional Sanger sequencing is performed on the following genes and exons:
    • MSH2 (NM_000251) 5
    • PMS2 (NM_000535) 7
    • PTEN (NM_000314) 9
  • Multiplex ligation-dependent probe amplification (MLPA) is performed on the following gene to call exon-level deletions and duplications:
    • PMS2 (NM_000535)

Sensitivity/Specificity

Clinical Sensitivity

Variable, dependent on phenotype

Analytic Sensitivity/Specificity

Variant Class Analytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region Analytic Specificity (NPA) Estimate (%)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

Exon-levelc deletions

97.8 (90.3-99.8) [2 exons or larger]

62.5 (38.3-82.6) [single exon]

>99.9

Exon-levelc duplications

83.3 (56.4-96.4) [3 exons or larger]

>99.9

Exon-level deletions/duplications (MLPA)

>99

>99

aPPA values are derived from larger methods-based MPS and/or Sanger validations. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA) unless otherwise indicated.

bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants

Limitations

  • A negative result does not exclude a heritable form of CNS cancer or other cancer.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if this patient has had an allogeneic stem cell transplantation.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of targeted gene(s)
    • Regulatory region and deep intronic variants
    • Breakpoints of large deletions/duplications
    • Sequence variants in EPCAM
  • The following exons are not sequenced due to technical limitations of the assay:
    • APC (NM_001354896) exon 12
    • APC (NM_001354898, NM_001354904) exon 2
    • APC (NM_001354900) exon 11
    • MEN1 (NM_001370251) exon 8
    • VHL (NM_001354723) exon 2
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by MPS
    • Large duplications less than 3 exons in size
    • Noncoding transcripts
    • Single exon deletions/duplications may not be detected based on the breakpoints of the rearrangement.
    • Low-level somatic variants
    • Certain other variants due to technical limitations in the presence of pseudogenes and/or repetitive/homologous regions
    • Deletions/duplications in the following exons:
      • APC (NM_001354896) 12
      • APC (NM_001354898, NM_001354904) 2
      • APC (NM_001354900) 11
      • MEN1 (NM_001370251) 8
      • PTEN (NM_000314, NM_001304718) 9
      • PTEN (NM_001304717) 1,10
      • RB1 (NM_000321) 22
      • SMARCE1 (NM_003079) 7,10-11
      • VHL (NM_001354723) 2
    • The following regions may have reduced sequencing sensitivity due to technical limitations of the assay:
      • RB1 (NM_000321) exon 22
      • SUFU (NM_016169, NM_001178133) exon 1

Genes Tested

To compare directly to other hereditary cancer panels offered by ARUP Laboratories, see the ARUP Hereditary Cancer Panel Comparison table.

Gene MIM Number Disorder/Associated Cancer(s)/Tumor(s) Inheritance

ALK

105590

ALK-related neuroblastic tumor susceptibility

Ganglioneuroblastoma, ganglioneuroma, neuroblastoma

AD

APC

611731

FAP

AFAP

GAPPS

Colorectal adenomas and cancer, duodenal adenomas and cancer, gastric fundic gland polyps, medulloblastoma, osteomas, pancreatic, thyroid, and others

AD

DICER1

606241

DICER1-related disorders

Pleuropulmonary blastoma, ovarian sex cord-stromal tumors, cystic nephroma, thyroid

AD

EPCAM

(Exon 9 deletion/duplications only)

185535

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreatic, prostate, renal pelvis and/or ureter, stomach, and others

AD

HRAS

190020

Costello syndrome

Neuroblastoma, rhabdomyosarcoma, transitional cell carcinoma of the bladder

AD

LZTR1

600574

Schwannomatosis

AD

Noonan syndrome

AR

MEN1

613733

MEN type 1

Adrenocortical, carcinoid, gastro-entero-pancreatic (GEP) neuroendocrine tumors, meningioma, parathyroid, pituitary, thyroid

AD

MLH1

120436

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD

CMMRD

AR

MSH2

609309

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD

CMMRD

AR

MSH6

600678

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD

CMMRD

AR

NF1

613113

NF1

Breast, GIST, gliomas, leukemia, malignant peripheral nerve sheath tumors, neurofibromas, pheochromocytoma

AD

NF2

607379

NF2

Astrocytoma, ependymoma, meningioma, schwannoma

AD

PMS2

600259

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD

CMMRD

AR

POT1

606478

POT1 tumor predisposition syndrome

Angiosarcoma, chronic lymphocytic leukemia, cutaneous melanoma, glioma

AD

PRKAR1A

188830

Carney complex

Endocrine tumor or overactivity, myxoma, schwannoma

AD

PTCH1

601309

NBCCS/Gorlin syndrome

Basal cell carcinoma, cardiac and ovarian fibromas, medulloblastoma

AD

PTEN

601728

Cowden syndrome/PTEN hamartoma tumor syndrome

Breast, colorectal, endometrial, Lhermitte-Duclos disease (cerebellar dysplastic gangliocytoma), melanoma,a renal cell carcinoma, thyroid, and others

AD

RB1

614041

Hereditary retinoblastoma

Melanoma,a osteosarcoma, pinealoblastoma, retinoblastoma, retinoma, soft tissue sarcoma

AD

SMARCA4

603254

Coffin-Siris syndrome, RTPS

Rhabdoid tumors located in CNS, kidney, ovary (SCCOHT), and others

AD

SMARCB1

601607

Coffin-Siris syndrome, RTPS

Rhabdoid tumors located in CNS, kidney, and others; schwannomatosis

AD

SMARCE1

603111

Coffin-Siris syndrome

Meningioma

AD

SUFU

607035

NBCCS/Gorlin syndrome

Basal cell carcinoma, cardiac and ovarian fibromas, medulloblastoma

AD

TP53

191170

LFS

Adrenocortical carcinoma, breast, choroid plexus carcinoma, CNS, colorectal, melanoma, osteosarcoma, pancreas, prostate, renal, rhabdomyosarcoma, soft tissue sarcoma, stomach, thyroid, and others

AD

TSC1

605284

TSC

Cardiac rhabdomyoma, fibromas, renal angiomyolipoma, retinal and other hamartomas, SEGA, and others

AD

TSC2

191092

TSC

Cardiac rhabdomyoma, fibromas, renal angiomyolipoma, retinal and other hamartomas, SEGA, and others

AD

VHL

608537

VHL syndrome

Endolymphatic sac tumors, epididymal and broad ligament cystadenomas, hemangioblastoma, neuroendocrine tumors, pheochromocytoma, renal cell carcinoma, retinal angioma

AD

aAssociation is suggested but not well-established at this time.

AD, autosomal dominant; AFAP, attenuated FAP; AR, autosomal recessive; CMMRD, constitutional mismatch repair deficiency; CNS, central nervous system; FAP, familial adenomatous polyposis; GAPPS, gastric adenocarcinoma and proximal polyposis of the stomach; GIST, gastrointestinal stromal tumor; HNPCC, hereditary nonpolyposis colorectal cancer; LFS, Li-Fraumeni syndrome; MEN, multiple endocrine neoplasia; NBCCS, nevoid basal cell carcinoma syndrome; NF1, neurofibromatosis type 1; NF2, neurofibromatosis type 2; RTPS, rhabdoid tumor predisposition syndrome; SCCOHT, small-cell carcinoma of the ovary, hypercalcemic type; SEGA, subependymal giant cell astrocytoma; TSC, tuberous sclerosis complex; VHL, Von Hippel-Lindau