Pediatric Cancer Panel

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
7973 ALK 81479,81479 Order Options and Pricing
ANKRD26 81479,81479
APC 81201,81203
ATM 81408,81479
AXIN2 81479,81479
BAP1 81479,81479
BLM 81479,81479
BMPR1A 81479,81479
CDC73 81479,81479
CDKN1C 81479,81479
CEBPA 81218,81479
DDX41 81479,81479
DICER1 81479,81479
DIS3L2 81479,81479
EPCAM 81479,81403
ETV6 81479,81479
EXT1 81479,81479
EXT2 81479,81479
FH 81405,81479
GATA2 81479,81479
GPC3 81479,81479
HRAS 81404,81479
KIF1B 81479,81479
MAX 81479,81479
MEN1 81405,81404
MLH1 81292,81294
MSH2 81295,81297
MSH6 81298,81300
NBN 81479,81479
NF1 81408,81479
NF2 81406,81405
PHOX2B 81404,81403
PMS2 81317,81319
POT1 81479,81479
PRKAR1A 81479,81479
PTCH1 81479,81479
PTCH2 81479,81479
PTEN 81321,81323
RB1 81479,81479
REST 81479,81479
RET 81406,81479
RUNX1 81479,81479
SAMD9L 81479,81479
SDHA 81406,81479
SDHAF2 81479,81479
SDHB 81405,81479
SDHC 81405,81404
SDHD 81404,81479
SMAD4 81406,81405
SMARCA4 81479,81479
SMARCB1 81479,81479
SMARCE1 81479,81479
SRP72 81479,81479
STK11 81405,81404
SUFU 81479,81479
TERC 81479,81479
TERT 81479,81479
TMEM127 81479,81479
TP53 81405,81479
TRIP13 81479,81479
TSC1 81406,81405
TSC2 81407,81406
VHL 81404,81403
WT1 81405,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
7973Genes x (64)81479 81201, 81203, 81218, 81292, 81294, 81295, 81297, 81298, 81300, 81317, 81319, 81321, 81323, 81403, 81404, 81405, 81406, 81407, 81408, 81479 $590 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available.

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Turnaround Time

18 days on average for standard orders or 14 days on average for STAT orders.

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Hereditary cancers in children have been observed in approximately 8-10% of diagnosed cancers (Coury et al. 2018. PubMed ID: 29750288). Hereditary cancers tend to occur at an earlier age (<45 years), ≥2 malignancies, consist of multiple affected family members including children, specific tumor types, children with excessive treatment toxicity, and can be associated with other congenital or other anomalies (Ripperger et al. 2017. PubMed ID: 28168833). The results of testing for a group of hereditary cancers can be important for counseling, screening, prevention, and treatment (Scollon et al. 2017. PubMed ID: 28357779; Coury et al. 2018. PubMed ID: 29750288).

Genetics

This test analyzes genes involved in hereditary solid and hematologic cancer syndromes which are mostly 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.

Pediatric cancers in this panel include: Acute Myeloid Leukemia, Colorectal, Endocrine, Medulloblastoma, Meningioma, Neurological, Nevoid Basal Cell Carcinoma, Osteosarcoma, Paraganglioma and Pheochromocytoma, Polyposis, Renal, Retinoblastoma, Rhabdoid, Rhabdomyosarcoma, Sarcoma, and Wilms Tumor.

See individual gene test descriptions for detailed information on clinical features, molecular biology of gene products, and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PG-Select

Genes tested in this panel have been implicated in hereditary pediatric solid and hematologic cancers, 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 hereditary cancers.

Clinical sensitivity for this panel is highly dependent on the type of cancer, specific ethnicity, and age of patients and is given based on more common hereditary cancer disorders found in children.

Familial Adenomatous Polyposis (FAP): Pathogenic APC sequence variants are found in >90% of individuals with FAP (Laken et al. 1999. PubMed ID: 10051640). Gross deletions/duplications have been reported in up to 12% of APC patients (Jasperson et al. 2017. PubMed ID: 20301519).

Constitutional Mismatch Repair Deficiency (CMMRD) Syndrome: Constitutional Mismatch Repair Deficiency Syndrome is mainly caused by biallelic germline pathogenic variants in PMS2 and MSH6, and less frequently in MSH2 and MLH1 (Rana and Syngal. 2017. PubMed ID: 28327367).

Hereditary Myelodysplastic Syndrome (MDS)/Acute Myeloid Leukemia (AML): in a recent study, pathogenic variants were identified in 29% of families with predisposition to MDS/AML (Churpek et al. 2015. PubMed ID: 26492932). The gene panel used in this study, however, did not include ANKRD26, SAMD9L, SRP72, DDX41, or ETV6 suggesting that 29% is a minimum value. Also, since we do not know all pathogenic variants in the MDS/AML predisposition genes, sensitivity of this test should steadily improve. To date, large deletions/duplications have not been reported in the ANKRD26, CEBPA, DDX41, ETV6, SAMD9L, or SRP72 genes in patients with Hereditary MDS/AML. Large deletions/duplications and complex rearrangements have been reported in patients with GATA2, RUNX1, TERC, TERT, and TP53 related syndromes and comprise ~ 9%, 29%, 5%, 5%, and 5%, respectively, of the different pathogenic variants reported for these genes (Human Gene Mutation Database).

Hereditary Neuroblastoma: ALK and PHOX2B germline pathogenic variants account for 90% of hereditary neuroblastoma, with the majority being in the ALK gene (Fisher and Tweddle. 2012. PubMed ID: 22673527). Clinical sensitivity for KIF1B pathogenic variants is unknown at this time since relatively few individuals with these variants have been reported.

Hereditary Paraganglioma-Pheochromocytoma Syndrome: Although the majority of hereditary paraganglioma-pheochromocytoma (PGL/PCC) syndrome tumors are sporadic (non-familial), approximately 13% of all PGL/PCC tumors are caused by germline pathogenic variants in known PGL/PCC syndrome genes (Welander et al. 2011. PubMed ID: 22041710).

Juvenile Polyposis Syndrome (JPS): This test is predicted to identify a pathogenic BMPR1A sequence variant in 11-22% and a pathogenic SMAD4 sequence variant in 20-26% of patients diagnosed with JPS. Deletion/duplication analysis is predicted to identify a BMPR1A pathogenic variant in 1-2% and a SMAD4 pathogenic variant in 2-9% of patients diagnosed with JPS (Larsen Haidle and Howe. 2017. PubMed ID: 20301642).

Li-Fraumeni Syndrome: Sequencing the TP53 gene can detect approximately 95% of patients with Li-Fraumeni syndrome. Deletions in the TP53 gene have been detected in 1% of Li-Fraumeni cases (Schneider et al. 2013. PubMed ID: 20301488).

Multiple Endocrine Neoplasia type 2 and Familial Medullary Thyroid Carcinoma: This test is predicted to detect pathogenic variants in >95% of cases (Marquard and Eng. 2015. PubMed ID: 20301434).

Peutz-Jeghers Syndrome: Approximately 55% of patients with a positive family history or 70% of patients with no family history of Peutz-Jeghers syndrome will be detected by STK11 sequencing. 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. 2016. PubMed ID: 20301443).

PTEN Hamartoma Syndrome: This test is predicted to detect causative PTEN pathogenic variants in ~80% of patients with Cowden syndrome (CS), ~65% of patients with Bannayan-Riley-Ruvalcaba syndrome (BRRS) and ~20% of patients with Proteus syndrome (PS). Large deletions are predicted to be detected in ~11% of patients with BRRS, but the sensitivity is not known for other PTEN related disorders (Eng 2003. PubMed ID: 12938083).

Testing Strategy

This panel typically provides ≥98% coverage of all coding exons of the genes listed, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.

The PHOX2B exon 3 polyalanine region is not covered.

This panel also includes testing for the inversion of exons 1-7 in MSH2.

Indications for Test

Young individuals with a clinical presentation of a cancer syndrome or a family history of cancer are candidates. Clinical presentation or family history includes early-onset cancer, multiple primary cancers, multiple family members with cancer, and co-morbidities. Earlier detection of tumors may lead to better outcomes (Coury et al. 2018. PubMed ID: 29750288). This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

Diseases

Name Inheritance OMIM ID
Acute Lymphoblastic Leukemia AD 613065
Adenomatous Polyposis Coli AD 175100
Adrenocortical Carcinoma, Hereditary AD 202300
Aml - Acute Myeloid Leukemia AD 601626
Ataxia-Pancytopenia Syndrome AD 159550
Ataxia-Telangiectasia Syndrome AR 208900
Atrial Myxoma, Familial AD 255960
Basal cell carcinoma 7 AR 614740
Beckwith-Wiedemann Syndrome AD 130650
Bloom Syndrome AR 210900
Bone Marrow Failure Syndrome 1 AD 614675
Carcinoid Tumors, Intestinal AD 114900
Carney Complex, Type 1 AD 160980
Choroid Plexus Papilloma AD 260500
Costello Syndrome AD 218040
Cowden Disease AD 158350
Cowden syndrome 3 AD 615106
Cowden-Like Syndrome AD 612359
Desmoid Disease, Hereditary AD 135290
Dyskeratosis Congenita Autosomal Dominant AD 127550
Dyskeratosis Congenita, Autosomal Dominant, 2 AD 613989
Exostoses, Multiple, Type I AD 133700
Exostoses, Multiple, Type II AD 133701
Familial Medullary Thyroid Carcinoma AD 155240
Glioma Susceptibility 9 AD 616568
Goiter, Multinodular 1, With Or Without Sertoli-Leydig Cell Tumors AD 138800
Gorlin Syndrome AD 109400
Hereditary Leiomyomatosis And Renal Cell Cancer AD 150800
Hereditary Mixed Polyposis Syndrome 2 AD 610069
Hereditary Nonpolyposis Colorectal Cancer Type 4 614337
Hereditary Nonpolyposis Colorectal Cancer Type 5 AD 614350
Hereditary Nonpolyposis Colorectal Cancer Type 8 613244
Juvenile Polyposis Syndrome AD 174900
Juvenile Polyposis/Hereditary Hemorrhagic Telangiectasia Syndrome AD 175050
Li-Fraumeni Syndrome AD 151623
Lynch Syndrome I AD 120435
Lynch Syndrome II AD 609310
Melanoma, Cutaneous Malignant, Susceptibility to, 10 AD 615848
Meningioma, Familial AD 607174
Mosaic Variegated Aneuploidy Syndrome 3 AR 617598
Muir-Torre Syndrome AD 158320
Multiple Endocrine Neoplasia, Type 1 AD 131100
Multiple Endocrine Neoplasia, Type 2A AD 171400
Multiple Endocrine Neoplasia, Type 2B AD 162300
Myeloproliferative/Lymphoproliferative Neoplasms, Familial (Multiple Types), Susceptibility to AD 616871
Neuroblastoma 1 AD 256700
Neuroblastoma 2 AD 613013
Neuroblastoma 3 613014
Neurofibromatosis, Familial Spinal AD 162210
Neurofibromatosis, Type 1 AD 162200
Neurofibromatosis, Type 2 AD 101000
Neurofibromatosis-Noonan Syndrome AD 601321
Nijmegen Breakage Syndrome AR 251260
Oligodontia-Colorectal Cancer Syndrome AD 608615
Paragangliomas 1 AD 168000
Paragangliomas 2 AD 601650
Paragangliomas 3 AD 605373
Paragangliomas 4 AD 115310
Paragangliomas 5 AD 614165
Parathyroid Carcinoma AD 608266
Perlman Syndrome AR 267000
Peutz-Jeghers Syndrome AD 175200
Pheochromocytoma AD 171300
Pigmented Nodular Adrenocortical Disease, Primary, 1 AD 610489
Pleuropulmonary Blastoma AD 601200
Retinoblastoma 180200
Rhabdoid Tumor Predisposition Syndrome 2 AD 613325
Rhabdomyosarcoma, embryonal, 2 AD 180295
Schwannomatosis 1 AD 162091
Simpson-Golabi-Behmel Syndrome AD 312870
Thrombocytopenia 2 AD 188000
Thrombocytopenia 5 AD 616216
Thrombocytopenia, Familial, With Propensity To Acute Myelogenous Leukemia AD 601399
Tuberous Sclerosis 1 AD 191100
Tuberous Sclerosis 2 AD 613254
Tumor Predisposition Syndrome AD 614327
Turcot Syndrome AR 276300
Von Hippel-Lindau Syndrome AD 193300
Wilms Tumor 6, Susceptibility to AD 616806
Wilms' Tumor 194070

Related Test

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PGxome®
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Citations

  • Churpek et al. 2015. PubMed ID: 26492932
  • Coury et al. 2018. PubMed ID: 29750288
  • Eng. 2003. PubMed ID: 12938083
  • Fisher and Tweddle. 2012. PubMed ID: 22673527
  • Human Gene Mutation Database (Biobase).
  • Jasperson et al. 2017. PubMed ID: 20301519
  • Laken et al. 1999. PubMed ID: 10051640
  • Larsen Haidle and Howe. 2017. PubMed ID: 20301642
  • Marquard and Eng. 2015. PubMed ID: 20301434
  • McGarrity et al. 2016. PubMed ID: 20301443
  • Rana and Syngal. 2017. PubMed ID: 28327367
  • Ripperger et al. 2017. PubMed ID: 28168833
  • Schneider et al. 2013. PubMed ID: 20301488
  • Scollon et al. 2017. PubMed ID: 28357779
  • Welander et al. 2011. PubMed ID: 22041710

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

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.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

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2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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