Disease (for NGS testing)

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the KCNH2, KCNQ1, RYR2 and TRDN genes is performed when NGS does not identify any pathogenic or likely pathogenic variants.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the DSP and PKP2 genes is performed when NGS does not identify any pathogenic or likely pathogenic variants.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the HNF1B gene is performed when NGS does not identify any pathogenic or likely pathogenic variants.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the ALMS1, BGN, DSP, KCNH2, KCNQ1, PKP2, RYR2 and TRDN genes is performed when NGS does not identify any pathogenic or likely pathogenic variants.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the ALMS1, DSP and PKP2 genes is performed when NGS does not identify any pathogenic or likely pathogenic variants. 

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the RYR2 and TRDN genes is performed when NGS does not identify any pathogenic or likely pathogenic variants.

ChromoSeqr is a whole genome sequencing assay intended for the comprehensive clinical genomic evaluation of known or suspected hematologic neoplasms including AML and MDS. ChromoSeq™ is capable of unbiased detection of chromosomal translocations, copy number alterations, single nucleotide variants, and insertions/deletions from DNA. The assay can also provide data in the setting of failed or incomplete cytogenetics.

ADAMTS13, C3, CD46, CFB, CFH, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CFI, DGKE, THBD; CFHR3-CFHR1 deletion by MLPA

Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region on the Illumina platform. Identified variants previously described and other potentially pathogenic non-synonymous variants are reported with interpretations. This targeted hybrid capture-based test is designed to detect somatic single nucleotide variants, insertions and deletions (indels). At a mean depth of coverage of at least 4000x across the captured region, this test has 89.84% sensitivity for variants at a variant allelic fraction (VAF) of 1.25% and 99.48% for variants at a VAF of at least 2.5%.

ACE, AGT, AGTR1, AHI1, BBS10, BICC1, CC2D2A, CEP290, CRB2, DNAJB11, EYA1, GANAB, GLIS2, HNF1B, INVS, IQCB1, NEK8, NPHP1, NPHP3, NPHP4, PAX2, PKD1, PKD2, PKHD1, REN, RPGRIP1L, SIX5, TMEM67, TTC21B, UMOD, USH2A and XPNPEP3

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the ALMS1 gene is performed when NGS does not identify any pathogenic or likely pathogenic variants.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the BGN gene is performed when NGS does not identify any pathogenic or likely pathogenic variants.Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the BGN gene is performed when NGS does not identify any pathogenic or likely pathogenic variants.

A tumor-only, high coverage targeted next generation sequencing assay for the identification of gene mutations, copy number alterations, microsatellite instability, tumor mutational burden, and gene fusions. The intended use of GatewaySeq is to provide a targeted genomic assessment of formalin or alcohol-fixed, paraffin-embedded surgical and cytological specimens from patients with solid tumors at initial diagnosis, relapse, or metastasis. GatewaySeq serves to identify the most common clinically significant mutations as an initial assay, and does not preclude additional, more comprehensive genomic profiling by other commercially available assays.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.

Next generation sequencing of all coding regions of 9 genes sequenced including FAS, JAK1, KRAS, NRAS, PIK3CD, PIK3R1, STAT5B, TLR8 and UBA1.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the KCNH2 and KCNQ1 genes is performed when NGS does not identify any pathogenic or likely pathogenic variants.

Next generation sequencing of all coding regions of 2 genes sequenced including IDH1 and IDH2.

Next generation sequencing of all coding regions of 5 genes sequenced including GNAS, HRAS, KRAS, NF1 and NRAS.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the HNF1B gene is performed when NGS does not identify any pathogenic or likely pathogenic variants.

A targeted sequencing assay for 49 genes and gene hotspots that are recurrently mutated in myeloid neoplasms, such as MDS and AML. This assay is intended to be used for both initial diagnosis and measurable/minimal residual disease (MRD) monitoring. MyeloSeq-HD uses a high coverage (12Gbases) unique molecular identifiers (UMIs)-based error corrected sequencing approach to achieve >95% sensitivity for previously identified mutations with VAFs ≥0.25%; sensitivity for newly detected variants is limited to 2% VAF. For post allogeneic hematopoietic stem cell transplant patients, MyeloSeq-HD can detect mixed chimerism.

ACE, ACTN4, ADCK4 (COQ8B), ANLN, APOL1, ARHGAP24, ARHGDIA, CD2AP, CLCN5, COL4A3, COL4A4, COL4A5, COQ2, COQ6, CRB2, CUBN, EMP2, FAT1, INF2, ITGA3, ITGB4, KANK1, KANK2, KANK4, LAGE3, LAMB2, LMX1B, MAGI2, MEFV, MYH9, MYO1E, NEIL1, NPHS1, NPHS2, NUP107, NUP205, NUP93, OCRL, OSGEP, PDSS2, PLCE1, PTPRO, REN, SCARB2, SMARCAL1, TP53RK, TPRKB, TRPC6, TTC21B, WDR73, WT1 and XPO5

Next generation sequencing of all coding regions of 28 genes sequenced including ABCA12, ACTB, ATP2A2, ATP2C1, BRAF, CARD14, EBP, FGFR1, FGFR2, FGFR3, GJB2, GNA11, GNA14, GNAQ, HRAS, KRAS,  KRT1, KRT10, KRT2, MAP3K3, MVD, NEK9, NRAS, NSDHL, PIK3CA, PMVK, PTCH1 and TEK.

Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. aCGH send out testing for the HNF1B gene is performed when NGS does not identify any pathogenic or likely pathogenic variants.

Focused Option: 1 gene: PIK3CA Comprehensive Option: 75 genes: ACTB, ACVRL1, AKT1, AKT2, AKT3, ARAF, BRAF, CCBE1, CCM2, CCND2, CDKN1C, CELSR1, CLDN14, CTNNB1, DCHS1, ELMO2, ENG, EPHB4, FAT4, FGFR1, FGFR2, FLT4, FOXC2, GATA2, GDF2, GJA4, GJC2, GLMN, GNA11, GNA14, GNAQ, GNAS, HGF, HRAS, IDH1, IDH2, KDR, KEL, KIF11, KRAS, KRIT1, LZTR1, MAP2K1, MAP2K2, MAP3K3, MET, MTOR, NF1, NF2, NRAS, PDCD10, PDGFRB, PIEZO1, PIK3CA,  PIK3CD, PIK3R1, PIK3R2, PRKACA, PTEN, PTPN11, PTPN14, RASA1, RHOA, SHOC2, SMAD3, SMAD4, SMO, SOS1, SOX18, SPRED1, STAMBP, TEK, TSC1, TSC2 and VEGFC). 

Next generation sequencing of all coding regions of 26 genes sequenced including BRAF, CBL, HRAS, KRAS, LZTR1, MAP2K1, MAP2K2, MAP3K3, MAP3K8, MRAS, NF1, NF2, NRAS, PPP1CB, PTPN11, RAF1, RASA1, RASA2, RIT1, RRAS2, SHOC2, SMAD4, SOS1, SOS2, SPRED1 and STAMBP.

Next generation sequencing of all coding regions of 49 genes sequenced including ACTB, AKT1, AKT2, AKT3, ARAF, BRAF, CCM2, CCND2, CDKN1C, DCHS1, EPHB4, FAT4, FGFR1, FGFR2, FLT4, GATA2, GJC2, GNA11, GNA14, GNAQ, HGF, HRAS, IDH1, IDH2, KIF11, KRAS, KRIT1, LZTR1, MAP2K1, MAP3K3, MET, MTOR, NF2, NRAS, PDGFRB, PIEZO1, PIK3CA, PIK3CD, PIK3R1, PIK3R2, PRKACA, PTEN, PTPN14, RASA1, SMAD3, SMO, TEK, TSC1 and TSC2.

Next generation sequencing of all coding regions of 6 genes sequenced including CDKN1C, GNA11, GNAQ, PIK3CA, PIK3R1 and TEK.

Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region on the Illumina platform. Identified variants previously described and other potentially pathogenic non-synonymous variants are reported with interpretations. This targeted hybrid capture-based test is designed to detect somatic single nucleotide variants, insertions and deletions (indels). At a mean depth of coverage of at least 4000x across the captured region, this test has 89.84% sensitivity for variants at a variant allelic fraction (VAF) of 1.25% and 99.48% for variants at a VAF of at least 2.5%.