Hereditary Pediatric Cancer Panel
Test code: ON0801
The Blueprint Genetics Hereditary Pediatric Cancer Panel analyzes 52 genes associated with inherited suscebtibility to pediatric cancer.
This Panel covers genes associated with a broad spectrum of hereditary cancer syndromes that may affect children. It has been estimated that around 1-10% of pediatric cancers are accounted for by these syndromes that have predominantly autosomal dominant inheritance pattern. The Hereditary Pediatric 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 is part of the Comprehensive Hereditary Cancer Panel.
About Hereditary Pediatric Cancer
Childhood leukemia is the most common pediatric cancer and accounts for more than a third of all new cancer diagnoses in children and adolescents. Most cancers occurring in children are thought to be sporadic and a genetic predisposition is rarely evoked. However, a small proportion of childhood leukemia and solid tumors can be caused by known hereditary cancer syndromes. The hereditary cancers that occur commonly in children include retinoblastoma (RB1), Wilms tumor (WT1) and medulloblastoma (SUFU). The main forms of hereditary cancer syndromes affecting children, adolescents, and yound adults are Li-Fraumeni syndrome (TP53), hereditary pheochromocytoma-paraganglioma (SDH genes), pleuropulmonaryblastoma tumor predisposition syndrome (DICER1), rhabdoid tumor of the kidney (SMARCB1) and multiple endocrine neoplasia (MEN1 and RET). In particular, when children present with adult type cancers, such as skin or gastrointestinal tract cancer, underlying genetic predisposition should be suspected. The risk of developing cancer in individuals carrying pathogenic germline mutations varies but can be as high as 80% for SDH and 100% for RET mutation carriers. Genetic testing for pediatric cancer patients has important implications on screening, prevention and treatment.
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: http://blueprintgenetics.com/faqs/#prenatal
|APC||Gardner syndrome, Desmoid disease, hereditary, Familial adenomatous polyposis||AD||294||1780|
|AXIN2||Oligodontia-colorectal cancer syndrome||AD||6||15|
|BAP1||Tumor predisposition syndrome||AD||13||73|
|BMPR1A*||Polyposis, juvenile intestinal||AD||38||108|
|CDC73||Carcinoma, parathyroid, Hyperparathyroidism, Hyperparathyroidism-jaw tumor syndrome||AD||23||86|
|CDKN1C||Beckwith-Wiedemann syndrome, IMAGE syndrome||AD||25||79|
|CEBPA||Acute myeloid leukemia, familial||AD||12||9|
|EPCAM||Diarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposis||AD/AR||15||63|
|FH||Hereditary leiomyomatosis and renal cell cancer||AD/AR||89||161|
|GATA2||Myelodysplastic syndrome, Chronic neutropenia associated with monocytopenia, evolving to myelodysplasia and acute myeloid leukemia, Acute myeloid leukemia, Emberger syndrome, Immunodeficiency||AD||19||76|
|HRAS||Costello syndrome, Congenital myopathy with excess of muscle spindles||AD||30||26|
|MEN1||Hyperparathyroidism, familial primary, Multiple endocrine neoplasia||AD||124||699|
|MLH1||Muir-Torre syndrome, Endometrial cancer, Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposis||AD/AR||670||1084|
|MSH2||Muir-Torre syndrome, Endometrial cancer, Colorectal cancer, hereditary nonpolyposis,, Mismatch repair cancer syndrome||AD/AR||646||1089|
|MSH6||Endometrial cancer, Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposis||AD/AR||308||426|
|NBN||Breast cancer, Nijmegen breakage syndrome||AD/AR||57||62|
|NF1*||Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndrome||AD||261||2607|
|NSD1||Sotos syndrome, Weaver syndrome, Beckwith-Wiedemann syndrome||AD||212||461|
|PHOX2B||Central hypoventilation syndrome, congenital, Neuroblastoma, susceptiblity to, Neuroblastoma with Hirschsprung disease||AD||5||70|
|PMS2*||Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposis||AD/AR||151||266|
|PRF1||Lymphoma, non-Hodgkin, Aplastic anemia, adult-onset, Hemophagocytic lymphohistiocytosis||AR||15||165|
|PRKAR1A||Myxoma, intracardiac, Acrodysostosis, Pigmented nodular adrenocortical disease, Carney complex||AD||50||173|
|PTCH1||Basal cell nevus syndrome||AD||46||348|
|PTEN*||Bannayan-Riley-Ruvalcaba syndrome, Lhermitte-Duclos syndrome, Cowden syndrome||AD||192||564|
|RECQL4||Baller-Gerold syndrome, RAPADILINO syndrome, Rothmund-Thomson syndrome||AR||34||92|
|RET||Hirschsprung disease, Central hypoventilation syndrome, congenital, Pheochromocytoma, Medullary thyroid carcinoma, Multiple endocrine neoplasia||AD/AR||80||405|
|RUNX1||Platelet disorder, familial, with associated myeloid malignancy||AD||13||74|
|SDHA*||Leigh syndrome/Mitochondrial respiratory chain complex II deficiency, Gastrointestinal stromal tumor, Paragangliomas, Dilated cardiomyopathy (DCM)||AD/AR||23||39|
|SDHB||Paraganglioma and gastric stromal sarcoma, Pheochromocytoma, Gastrointestinal stromal tumor, Paragangliomas, Cowden-like syndrome||AD||72||249|
|SDHC||Paraganglioma and gastric stromal sarcoma, Gastrointestinal stromal tumor, Paragangliomas||AD||14||53|
|SDHD||Paraganglioma and gastric stromal sarcoma, Pheochromocytoma, Paragangliomas, Carcinoid tumors, intestinal, Cowden syndrome||AD||42||158|
|SMAD4||Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasia||AD||119||128|
|SMARCB1||Schwannomatosis, Rhabdoid tumor predisposition syndrome||AD||17||115|
|SUFU||Medulloblastoma, Basal cell nevus syndrome||AD||7||27|
|TP53||Colorectal cancer, Li-Fraumeni syndrome, Ependymoma, intracranial, Choroid plexus papilloma, Breast cancer, familial, Adrenocortical carcinoma, Osteogenic sarcoma, Hepatoblastoma, Non-Hodgkin lymphoma||AD||148||391|
|TSC1||Lymphangioleiomyomatosis, Tuberous sclerosis||AD||61||306|
|TSC2||Lymphangioleiomyomatosis, Tuberous sclerosis||AD||141||977|
|VHL||Erythrocytosis, familial, Pheochromocytoma||AD/AR||143||573|
|WT1||Denys-Drash syndrome, Frasier syndrome, Wilms tumor||AD||23||165|
*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.
|Gene||Genomic location HG19||HGVS||RefSeq||RS-number||Comment||Reference|
Blueprint Genetics offers a comprehensive Hereditary Pediatric Cancer Panel that covers classical genes associated with Beckwith-Wiedemann syndrome, Bloom syndrome, familial adenomatous polyposis, Gorlin syndrome, hereditary nonpolyposis colon cancer, hereditary paraganglioma-pheochromocytoma, hereditary retinoblastoma, juvenile polyposis syndrome, Li-Fraumeni syndrome, medulloblastoma predisposition, multiple endocrine neoplasia, nephroblastoma, neurofibromatosis type 1, neurofibromatosis type 2, pediatric cancer, 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.
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. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. 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.
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.
Choose an analysis method
ICD & CPT codes
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.