RenaDx®: Comprehensive Renal Disease Panel

Methodology

Targeted Exome/ Slice Exome (Next Generation Sequencing including Copy Number Variation)

Coverage

120x

Assay Information
- ABCC6: Deletion/duplication and sequencing analysis is not offered for exons 1-9.
- AMN: Deletion/duplication analysis is not offered for exon 1.
- ARHGAP24: Deletion/duplication analysis is not offered for exon 10.
- BBS9: Deletion/duplication analysis is not offered for exon 4.
- CEP290: Analysis includes the intronic variant NM_025114.3:c.2991+1655A>G.
- CFH: Deletion/duplication analysis is not offered for exons 20| 22 and sequencing analysis is not offered for exons 15| 20| 22.
- CISD2: Deletion/duplication and sequencing analysis is not offered for exon 3.
- CLCNKB: Deletion/duplication analysis is not offered for this gene.
- COL4A4: Deletion/duplication analysis is not offered for exon 27.
- COX10: Deletion/duplication and sequencing analysis is not offered for exon 6.
- CRB2: Deletion/duplication analysis is not offered for exons 5-6.
- CUBN: Analysis includes the intronic variant NM_001081.3: c.3330-439C>G.
- DICER1: Sequencing analysis for exons 22 includes only cds +/- 10 bp.
- ENPP1: Sequencing analysis for exons 2 includes only cds +/- 5 bp.
- FN1: Sequencing analysis for exons 14 includes only cds +/- 10 bp.
- GLA: Analysis includes the intronic variant NM_000169.2:c.IVS4+919G>A.
- GNA11: This test is not validated to detect or quantify variant mosaicism and caution should be used while interpreting results for this gene in which mosaicism or somatic variation is an established cause of disease.
- GNAS: This test is not validated to detect or quantify variant mosaicism and caution should be used while interpreting results for this gene in which mosaicism or somatic variation is an established cause of disease.
- GPC3: Sequencing analysis for exons 3 includes only cds +/- 10 bp.
- KANK1: Sequencing analysis for exons 9 includes only cds +/- 0 bp.
- KANSL1: Deletion/duplication and sequencing analysis is not offered for exons 2-3.
- KLHL3: Sequencing analysis for exons 6 includes only cds +/- 0 bp.
- NF1: Sequencing analysis for exons 2| 7| 25| 41| 48 includes only cds +/- 10 bp.
- NOTCH2: Deletion/duplication and sequencing analysis is not offered for exons 1-4.
- NUP107: Deletion/duplication analysis is not offered for exon 8.
- NUP160: Deletion/duplication analysis is not offered for exon 33.
- NUP85: Deletion/duplication analysis is not offered for exon 4.
- NXF5: Deletion/duplication and sequencing analysis is not offered for exons 7-13.
- PDSS1: Deletion/duplication analysis is not offered for exon 2.
- PHEX: Analysis includes the NM_000444.5:c.*231A>G variant.
- PKHD1: Deletion/duplication analysis is not offered for exon 13.
- PLG: Deletion/duplication analysis is not offered for exon 1.
- PRODH: Deletion/duplication analysis is not offered for exons 8| 12.
- ROBO1: Deletion/duplication analysis is not offered for exon 31.
- SEC63: Sequencing analysis for exons 4| 13 includes only cds +/- 0 bp.
- SI: Deletion/duplication analysis is not offered for exon 7.
- TSC1: Sequencing analysis for exons 21 includes only cds +/- 10 bp.

Reflex Test

RenaXome®

Ordering information

Turnaround Time: 10 business days

Preferred Speciment: Saliva Kits (available upon request)

Alternate Specimens: Nail clippings or 3-mL whole blood in purple top EDTA tube

Request a specimen collection kit

Limitations

All sequencing technologies have limitations. A negative result from this analysis does not rule out a possible genetic diagnosis as some variants may not be detected by this test. This test is not designed to detect low level mosaicism, structural rearrangements, indels >40bp, deep intronic variants of unknown clinical significance, or large cytogenetic CNVs. Certain inherent qualities of the human genome, for example repetitive regions/homopolymers, GC rich, pseudogenes, and rare polymorphisms, pose significant technical challenges such as sequence misalignment that may potentially impact the accuracy of the results. False negative results may also occur in the setting of allogeneic bone marrow, stem cell transplantation, active or chronic hematologic conditions, recent blood transfusions, suboptimal DNA quality or PCR trace contamination. Other potential sources of error include sample mix-ups and clerical issues.

References
- 1. Richards S et al. Genetics in medicine. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. 2015 May;17(5):405-24 (PMID: 25741868)
- 2. GnomAD (gnomAD)
- 3. CSPEC (ClinGen variant classification rules registry) Criteria Specification Registry
- 4. Normal copy number variation in healthy individuals database of genomic variants: http://dgv.tcag.ca/dgv/app/home
- 5. Riggs, E.R., Andersen, E.F., Cherry, A.M. et al. Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med 22, 245–257 (2020). https://doi.org/10.1038/s41436-019-0686-8
- 6. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan 1;42(1):D980-5. doi: 10.1093/nar/gkt1113. PubMed PMID: 24234437.
- 7. Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), Copyright® 1966-2012. World Wide Web URL: http://omim.org.
- 8. http://tinyurl.com/ACMGv4 (ACMG/ Clingen draft Interpretation SOP); clingen_variant-curation_sopv1.pdf

Tagged Genes

Primary panel:

449 genes selected

ABCC6 ABCC8 ACE ACTB ACTG1 ACTN4 ACVRL1 ADA2 ADAMTS13 ADAMTS9 ADCY10 AGPAT2 AGT AGTR1 AGXT AHI1 ALG1 ALG5 ALG8 ALG9 APOA4 ALMS1 ALPL AMN ANKS6 ANLN ANOS1 AP2S1 APOA1 APOC2 APOPT1 APOE APOL1 APRT AQP2 ARHGDIA ARL6 ARL13B ATP6V0A4 ATP6V1B1 ATP7B AVP AVPR2 B2M B9D1 BBIP1 BBS1 BBS10 BBS12 BBS2 BBS4 BBS5 BBS7 BBS9 BCS1L BICC1 C3AR1 C8ORF37 BMP4 BMPR2 BNC2 BRAF BSCL2 BSND C1QB C3 CEP164 CA2 CACNA1H CFAP47 CACNA1S CASR CFD CAV1 CC2D2A CFHR1 CFHR2 CFHR3 CFHR4 CD151 CD2AP CD46 CDC73 CDKN1C CEL CEP290 CEP83 CFB CFH CFHR5 CFI COPA CHD7 CHRNA3 CISD2 CDK20 CLCN2 CLCN5 COX20 CLCNKA CLCNKB CLDN16 CLDN19 CNNM2 COL4A1 COL4A3 COL4A4 COL4A5 COQ2 COQ6 COQ8B COX10 CPLANE1 CPT2 CRB2 CREBBP CTNS DKC1 CUBN CUL3 CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP24A1 CYP27B1 CYP2R1 CYS1 DCDC2 DGKE DHCR7 DLC1 DMP1 DNAJB11 DNASE1L3 DSTYK DZIP1L EBP EHHADH EIF2AK3 ELP1 ENPP1 ESCO2 EYA1 KCNJ16 FAH FAM186B FAM20A FAN1 FANCA FANCB FANCC FANCD2 FANCE FANCF FANCG G6PC FANCI FANCL FANCM FASTKD2 FAT1 FAT4 FGA GDF2 FGF10 FGF23 FGFR1 FGFR2 FLCN FN1 FOXC1 FOXC2 FOXI1 FOXP3 FRAS1 FREM1 FREM2 FXYD2 GALNT3 GANAB GATA3 GATM GCK GCM2 GLA GLI3 GLIS2 GLIS3 GNA11 GNAS GPC3 GPHN GREB1L GREM1 GRHPR GRIP1 GSN HBB HGD HNF1A HNF1B HNF4A HOGA1 HOXA13 HPRT1 HPS1 HPSE2 HSD11B2 HSD3B2 IFT122 IFT140 IFT172 IFT43 IFT80 INCENP INF2 INPP5E INS INVS IQCB1 ITGA3 ITGA6 ITGB4 ITSN1 ITSN2 JAG1 KANK1 KANK2 KANK4 KANSL1 KAT6B KCNA1 KCNJ1 KCNJ10 KCNJ11 KCNJ5 KCNK3 KCTD1 KDM6A MMADHC KIF14 KIF7 KLHL3 KMT2D KRAS KYNU LAGE3 LAMA5 LAMB2 LCAT LDHA LIFR LMNA LMX1B LPIN1 LRP2 LRP4 LRP5 LYZ LZTFL1 MAFB SON MAGED2 MAGI2 MAP2K1 MAP2K2 MAPKBP1 MEFV MKKS MKS1 MMAA MMAB MMACHC MNX1 MOCOS MOCS1 MOCS2 MUC1 MVK MYCN MYH9 MYO1E NEK1 NEK8 NEU1 NEUROD1 NF1 NHERF1 NIPBL VTN NLRP3 NOTCH2 NPHP1 NPHP3 NPHP4 NPHS1 NPHS2 NR0B1 NR3C1 NR3C2 NSD1 NSDHL NUP107 NUP133 NUP160 NUP205 ZEB2 NUP85 NUP93 NXF5 OCRL OFD1 OPLAH OSGEP PAX2 PBX1 PCBD1 PDSS1 PDSS2 PDX1 PEX6 PGK1 PHEX PHF6 PIAS1 PIK3CA PKD1 PKD2 PKHD1 PLCE1 PLG PMM2 POC1B PODXL PREPL PRKCSH PRODH PROKR2 PRPS1 PTH1R PTPN11 PTPRO PUF60 PYGM RAD51C RBM48 RCOR1 REN RET RMND1 ROBO2 ROR2 RPGRIP1L RPS19 RRM2B SALL1 SALL4 SARS2 SCARB2 SCN4A SCNN1A SCNN1B SCNN1G SDCCAG8 SEC61A1 SEC61B SEC63 SGPL1 SI SIX1 SLC12A1 SLC12A3 SLC9A3R1 SLC17A5 SLC19A2 SLC22A12 SLC26A1 SLC2A2 SLC2A9 SLC34A1 SLC34A3 SLC37A4 SLC3A1 SLC4A1 SLC4A4 SLC5A1 SLC5A2 SLC6A19 SLC7A7 SLC7A9 SLX4 SMAD9 SMARCAL1 SMC1A SOX11 SOX17 SOX18 SRCAP STAR STX16 TACO1 TBC1D8B TCTN2 TFAP2A THBD TMEM138 TMEM216 TMEM231 TMEM237 TMEM67 TNS2 TNXB TP53RK TP63 TPRKB TRPC6 TRIM32 TRIM8 TRPM6 TSC1 TSC2 TTC8 TTR TXNDC15 TXNL4A UMOD VDR VHL VPS33B VIPAS39 WAS WDR4 WDR19 WDR72 WDR34(DYNC2I2) WDR35 WDPCP WDR73 WFS1 WNK1 WNK4 WNT5A WT1 XDH XPNPEP3 XPO5 XRCC4 ZNF423

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Test Description

Methodology

Coverage

Assay Information

Reflex Test

Ordering information

Limitations

References

Tagged Genes