Comprehensive Pediatric Solid Tumor Panel

About Pediatric Solid Tumors

Solid tumors account for 60% of the diagnosed pediatric malignancies. This heterogenous group of tumors are derived from several diverse cell types and affect various organ systems.¹ Within the spectrum of pediatric solid tumors, hereditary pediatric cancer syndromes account for approximately 8-10% of all diagnoses.² These cancer syndromes are characterized by earlier onset (often before age 45), multiple primary malignancies in the same individual, and multiple affected family members including children.³ This panel covers a comprehensive list of genes associated with hereditary pediatric cancer syndromes including, but not limited to, central nervous system tumors such as medulloblastomas or gliomas, neuroendocrine tumors, retinoblastomas, and sarcomas. This panel analyzes high-risk genes which can confer a substantially increased lifetime risk of cancer, moderate-risk genes which are associated with moderately increased lifetime risks, and genes for which there is emerging evidence of their risk for cancer compared to the general population. Most hereditary pediatric cancer syndromes follow an autosomal dominant inheritance pattern though some genes (such as BLM) demonstrate autosomal recessive inheritance. Furthermore, while most pathogenic variants are inherited, de novo variants can occur, particularly in genes like PTEN and TP53. Assessment of multiple genes associated with hereditary cancer can be useful in determining personal or familial risks and can identify more clinically significant findings compared to single gene or single syndrome testing due to the genetic heterogeneity associated with each cancer type.⁴ Causative variants can include both sequence variants and copy number variations, with some conditions showing specific patterns in the distribution of variant types. Diagnostic yields vary by cancer type, with some syndromes showing high detection rates while others demonstrate moderate to low detection rates. The diagnostic yield of this panel varies significantly based on syndrome and clinical presentation.^5,6

All genetic tests have limitations. Please refer to our Test Methods page for limitations relevant to this methodology.

EPCAM, GREM1: Only copy number variant analysis is reported.

FLCN: This test does not include analysis of FLCN (NM_144997.5) non-coding exons 1, 2, and 3. To our knowledge, no sequence variants have been reported in association with FLCN-related disease within this interval. However, a limited number of copy number variants (CNVs) have been reported in association with Birt-Hogg-Dubé syndrome (BHDS) within this interval (e.g. Benhammou et al. 2011. PubMed ID: 21412933, Table 1; Zhang et al. 2016. PubMed ID: 27229674; Enomoto et al. 2020. PubMed ID: 31778855). If BHDS is strongly suspected, aCGH may be ordered using test code 600.

MITF: Testing for MITF is restricted to c.952G>A (p.318K).

MSH3: Variants in the MSH3 gene (NM_002439.4) within c.151_210 are not reported due to technical difficulties.

PHOX2B: The PHOX2B exon 3 polyalanine region is not covered.

PIK3CA: This test does not detect low levels of mosaicism that may be associated with somatic PIK3CA-related overgrowth and similar disorders. If the index of suspicion for somatic mutation is high, we recommend testing affected tissues using a deep sequencing platform with higher sensitivity for low-level mosaics such as the Somatic Overgrowth and Vascular Malformations Panel offered by University of Pennsylvania.

PMS2: DNA analysis of the PMS2 gene is complicated due to the presence of several pseudogenes. One particular pseudogene, PMS2CL, has high sequence similarity to PMS2 exons 11 to 15 (Blount et al. 2018. PubMed ID: 29286535). Next-generation sequencing (NGS) based copy number variant (CNV) analysis can detect deletions and duplications involving exons 1 to 10 of PMS2 but has less sensitivity for exons 11 through 15. Multiplex ligation-dependent probe amplification (MLPA) can detect deletions and duplications involving PMS2 exons 1 to 15. Of note, PMS2 MLPA is not typically included in this test but can be ordered separately using test code 6062, if desired.

POLD1, POLE: Testing is restricted to the clinically relevant exonuclease domains.

SDHA: Next Generation Sequencing analysis of this gene is technically challenging due to the presence of segmental duplications and paralogy. Therefore, analysis of CNVs in this gene is not included in this test.

TSC1: This test does not include analysis of TSC1 (NM_000368.4) non-coding exons 1 and 2 as to our knowledge, no sequence variants have been reported in association with TSC1-related disease within this region. However, a limited number of copy number variants (CNVs) have been reported in association with tuberous sclerosis complex (TSC) within this interval (e.g. van den Ouweland et al. 2011. PubMed ID: 20877415; Overwater et al. 2016. PubMed ID: 27406250). If TSC is strongly suspected, TSC1 multiplex ligation-dependent probe amplification (MLPA) may be ordered using test code 2055.

Enhanced Testing

APC: This testing includes APC promoter 1B.

MSH2: This testing includes the inversion of exons 1 to 7 in MSH2 (Boland Inversion) and the c.942+3A>T polyalanine repeat variant.

NF1, PMS2, STK11: Deletion and duplication testing for NF1, PMS2, and STK11 is performed using NGS, but CNVs detected in these genes are usually confirmed via multiplex ligation- dependent probe amplification (MLPA).

PTEN: This testing includes coverage of the PTEN minimal promoter region (positions –1239 to –765 relative to the start codon).

VHL: This testing includes the VHL E1’ cryptic exon.

The analytical sensitivity of the PGxome platform has been validated at >99% for single nucleotide variants, >95% for indels <49 bp, and >99% for CNV ≥3 exons in size. Sensitivity is reduced in regions with repetitive elements or paralogy.

PGxome® platform: Capture and amplification based Next Generation Sequencing (NGS) is used to sequence the coding regions of nearly all genes and immediate flanking non-coding DNA (± 10 bp) in all available transcripts along with other non-coding regions harboring known disease-causing variants. Results are filtered to defined genes in panel. Reportable variants include both sequence variants and NGS-based detection of copy number variants (CNVs).

Variants not meeting our quality threshold through NGS alone are confirmed with an orthogonal method, including but not limited to Sanger and array.

All variants within the analyzed genes which are classified as pathogenic, likely pathogenic, risk, or variant of uncertain significance will be reported.