Hereditary Renal Cancer Panel

26 gene panel that includes assessment of non-coding variants

Ideal for patients with a clinical suspicion of hereditary renal cancer. This panel is designed to detect heritable germline mutations and should not be used for the detection of somatic mutations in tumor tissue.

Analysis methods Availability Number of genes Test code CPT codes
PLUS
SEQ
DEL/DUP
4 weeks 26 GHC0098 SEQ 81321
SEQ 81404
SEQ 81405
DEL/DUP 81479

Summary

Sample requirements:

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • 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.

About

The main inherited forms of renal cell cancer and the associated genes include von Hippel-Lindau disease (VHL), hereditary papillary renal cancer (MET), hereditary leiomyomatosis and renal cancer (FH), familial renal cancer (BAP1), Birt-Hogg-Dube syndrome (FLCN), and renal cancer associated with tuberous sclerosis (TSC1, TSC2). In general, hereditary renal cancer cases present with an earlier age of onset and are more likely to involve bilateral tumors. Other neoplasms may also occur. The risk of developing renal cancer associated with these syndromes varies but can be as high as 67% for patients with hereditary papillary renal cancer. Germline mutations in WT1 are associated with Wilms tumor, one of the most common solid tumors of childhood, occurring in 1 in 10,000 children and accounting for 8% of childhood cancers. The prevalence of individual hereditary renal cancer syndromes varies from very rare to 3:100,000.

Panel Content

Genes in the Hereditary Renal Cancer Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
BAP1Tumor predisposition syndromeAD52106
CDC73Carcinoma, parathyroid, Hyperparathyroidism, Hyperparathyroidism-jaw tumor syndromeAD4290
CDKN1CBeckwith-Wiedemann syndrome, IMAGE syndromeAD2881
DICER1DICER1 syndromeAD177126
DIS3L2Perlman syndromeAR1011
EPCAMDiarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposisAD/AR2675
FHHereditary leiomyomatosis and renal cell cancerAD/AR156205
FLCNBirt-Hogg-Dube syndrome, Pneumothorax, primary spontaneousAD139190
GPC3Simpson-Golabi-Behmel syndromeXL2972
METDeafness, Renal cell carcinoma, papillary, Osteofibrous dysplasia, susceptibility toAD/AR2029
MLH1Muir-Torre syndrome, Endometrial cancer, Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR8291174
MSH2Muir-Torre syndrome, Endometrial cancer, Colorectal cancer, hereditary nonpolyposis,, Mismatch repair cancer syndromeAD/AR8741224
MSH6Endometrial cancer, Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR580569
PMS2Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR259324
PTENBannayan-Riley-Ruvalcaba syndrome, Lhermitte-Duclos syndrome, Cowden syndromeAD398627
RESTFibromatosis, gingival, 5AD315
SDHBParaganglioma and gastric stromal sarcoma, Pheochromocytoma, Gastrointestinal stromal tumor, Paragangliomas, Cowden-like syndromeAD138262
SDHCParaganglioma and gastric stromal sarcoma, Gastrointestinal stromal tumor, ParagangliomasAD2657
SDHDParaganglioma and gastric stromal sarcoma, Pheochromocytoma, Paragangliomas, Carcinoid tumors, intestinal, Cowden syndrome, Mitochondrial complex II deficiencyAD62164
SMARCA4Rhabdoid tumor predisposition syndromeAD5555
SMARCB1Schwannomatosis, Rhabdoid tumor predisposition syndromeAD31116
TP53Colorectal cancer, Li-Fraumeni syndrome, Ependymoma, intracranial, Choroid plexus papilloma, Breast cancer, familial, Adrenocortical carcinoma, Osteogenic sarcoma, Hepatoblastoma, Non-Hodgkin lymphomaAD372481
TSC1Lymphangioleiomyomatosis, Tuberous sclerosisAD138346
TSC2Lymphangioleiomyomatosis, Tuberous sclerosisAD3221137
VHLErythrocytosis, familial, PheochromocytomaAD/AR188595
WT1Denys-Drash syndrome, Frasier syndrome, Wilms tumor, Nephrotic syndrome, type 4AD36175

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
CDKN1CChr11:2905209c.*5+20G>TNM_000076.2rs760540648
EPCAMChr2:47606078c.556-14A>GNM_002354.2rs376155665
MLH1Chr3:37035012c.-27C>ANM_000249.3rs587779001
MLH1Chr3:37034997c.-42C>TNM_000249.3rs41285097
MLH1Chr3:37038099c.117-11T>ANM_000249.3rs267607711
MLH1Chr3:37070436c.1558+13T>ANM_000249.3rs267607834
MLH1Chr3:37050292c.454-13A>GNM_000249.3rs267607749
MLH1Chr3:37053487c.589-9_589-6delGTTTNM_000249.3rs752286654,rs587779026
MLH1Chr3:37061788c.885-9_887dupTCCTGACAGTTTNM_000249.3rs63751620
MSH2Chr2:47630150c.-181G>ANM_000251.2rs786201698
MSH2Chr2:47630106c.-225G>CNM_000251.2rs138068023
MSH2Chr2:47630251c.-78_-77delTGNM_000251.2rs587779182
MSH2Chr2:47635062c.212-478T>GNM_000251.2rs587779138
MSH6Chr2:48034014c.*15A>CNM_000179.2
PTENChr10:89623226c.-1001T>CNM_000314.4
PTENChr10:89623116c.-1111A>GNM_000314.6
PTENChr10:89623056c.-1171C>TNM_000314.6rs587779981
PTENChr10:89623049c.-1178C>TNM_000314.6
PTENChr10:89622988c.-1239A>GNM_000314.6
PTENChr10:89623462c.-765G>ANM_000314.4
PTENChr10:89623365c.-862G>TNM_000314.4rs587776675
PTENChr10:89622883–89623482
PTENChr10:89623373c.-854C>GNM_000314.4
PTENChr10:89623331c.-896T>CNM_000314.4
PTENChr10:89623306c.-921G>TNM_000314.4
PTENChr10:89623296c.-931G>ANM_000314.4rs587781959
PTENChr10:89692749c.254-21G>CNM_000314.4
SMARCB1Chr22:24176437c.*70C>TNM_003073.3
SMARCB1Chr22:24176449c.*82C>TNM_003073.3
SMARCB1Chr22:24176316c.1119-12C>GNM_003073.3
TP53Chr17:7590694c.-29+1G>TNM_000546.5
TSC2Chr16:2098067c.-30+1G>CNM_000548.3rs587778004
TSC2Chr16:2127477c.2838-122G>ANM_000548.3
TSC2Chr16:2138031c.5069-18A>GNM_000548.3rs45484794
TSC2Chr16:2110656c.976-15G>ANM_000548.3rs45517150
VHLChr3:10183453c.-75_-55delCGCACGCAGCTCCGCCCCGCGNM_000551.3rs727503744

Panel Update

Genes added

  • REST
  • SMARCA4

Genes removed

  • HNF1A

Test strength and Limitations

The strengths of this test include:

  • CAP and ISO-15189 accreditations covering all operations at GHC Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in GHC WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: *PPA2* (11, 12). Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:
  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than GHC Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

Test Performance

The GHC Genetics panel covers classical genes associated with Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia (CPVT), cardiac arrest underlying cardiac condition, cardiac arrest cause unspecified, syncope and collapse, abnormal ECG, Long QT syndrome, arrhythmogenic right ventricular cardiomyopathy (ARVC) and Short QT syndrome. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. GHC Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient’s phenotype is suggestive of a specific mutation type.

Performance of GHC Genetics Whole Exome Sequencing (WES) assay.
All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
The performance presented above reached by WES with the following coverage metrics
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Detection of Del/Dup of several genes is by MLPA analysis (MS Holland). All genes are performed by CNV analysis through the genome depending on exon size, sequencing coverage and sequence content. We have validated the assays for different starting materials including isolated DNA from EDTA blood that provide high-quality results.

Bioinformatics & clinical interpretation

The sequencing data generated in our laboratory is analysed by our bioinformatic pipeline, integrating state-of-the art algorithms and industry-standard software solutions. We use also JSI medical systems software for sequencing data analysis. JSI medical systems is a certified system offering sophisticated bioinformatic software solutions covering a wide field of sequencing techniques.

Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results.

Every pathogenic or probably pathogenic variant is confirmed by the Sanger sequencing method. 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. The analysis of detected variants was performed on the basis of the reference database of polymorphisms and international mutation databases: UMD, LOVD and ClinVar.

The consequence of variants in coding and splice regions are estimated using Alamut software. The Alamut database contains more than 28000 coding genes, non-protein coding genes and pseudogenes. This database (shared with the high throughput annotation engine for NGS data, Alamut Batch) is frequently updated. Information comes from different public databases such as NCBI, EBI, and UCSC, as well as other sources including gnomAD, ESP, Cosmic, ClinVar, or HGMD and CentoMD (for those a separate subscription from Qiagen/Biobase and Centogene respectively is required). Alamut Visual finds information about nucleotide conservation data through many vertebrates’ species, with the phastCons and phyloP scores, amino acid conservation data through orthologue alignments and information on protein domains.

Moreover, we integrate several missense variant pathogenicity prediction tools and algorithms such as SIFT, PolyPhen, AlignGVGD or MutationTaster. It also offers a window dedicated to the in silico study of variants’ effect on RNA splicing, allowing the assessment of their potential impact on splice junctions and visualization of cryptic or de novo splice sites. Impact on splicing regulation is also assessed.


Clinical interpretation

At GHC 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 report. We recommend an interpretation of the findings of this molecular genetic analysis, including subsequent oncological consultation for the patient in the context of genetic counselling for the patient.

We strive to continuously monitor current genetic literature identifying new relevant information and findings and adapting them to our diagnostics. This enables relevant novel discoveries to be rapidly translated and adopted into our ongoing diagnostics development without delay. The undertaking of such comprehensive due diligence ensures that our diagnostic panels and clinical statements are the most up-to-date on the market.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analysed at our laboratories enables us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant three times at GHC Genetics. Reported variants of uncertain significance (VUS) are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size >10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at GHC Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counselling.

Our Clinical interpretation team analyses millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratories are therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by GHC Genetics is re-classified, our laboratories will issue a follow-up statement to the original ordering health care provider at no additional cost.