Technique

Pan - T cell - thymic and peripheral T lymphocytes, mast cells, NK cells, T cell lymphoma subsets

Normal follicular dendritic cells; dendritic cell tumor/sarcomas, B cell subset

B-CLL, Small lymphocytic (B cell) lymphoma

Normal and neoplastic T cells

Mononuclear Hodgkin's cells, Reed Sternberg cells of Hodgkin's lymphoma and anaplastic large cell lymphoma; plasma cells

Endothelium, vascular neoplasms, plasma cells

Myeloid progenitor cells, endothelium, vascular tumors

Neural and neuroendocrine tumor, soft tissue tumor subset, NK cells, plasma and T-cell subsets

Neural and neuroendocrine tumor, follicular center cell lymphoma

Megakaryocytes, platelets

Macrophages

Macrophages

Thymocytes and mature T cells

Pan B cells

Cytotoxic / suppressor T cells

T cells, cortical thymocytes, Ewing's sarcoma / PNET, sex cord stromal tumors

Detection of gains or losses of the CDKN2A gene region

Detection of gains or losses of the CDKN2A gene region or centromere of chromosome 9

Enteric differentitation, GI tumors, colorectal carcinoma, GI origin of metastatic adenocarcinomas and carcinoids. Mucinous carcinomas of the ovary

Detects aneuploidy of chromosome 8

Detects percentage of donor vs. recipient cells in gender mismatched transplants

Neuroendocrine neoplasms

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.

Detects amplification or deletion at 1p32.3 and 1q21

Detects common gene rearrangements associated with CLL: CEP12, D13S319 del13q, ATM 11q22.3, TP53 17p13, CCND1/IGH t(11;14) BCL6 3q27

Detects common gene rearrangements associated with CML: BCR/ABL t(9;21), FIP1L1/PDGFRA CHIC2/del 4q12

Acid mucopolysaccharides and sialomucins

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

Demonstrtion of amyloid in tissues

Affymetrix CytoScan HD assay with genomic DNA extraction to detect small gains and losses across the entire genome. A genomic imbalance is ALWAYS REPORTED when deletions are greater than 200 kb and duplications are greater than 500 kb, unless they represent a region clearly associated with benign copy number polymorphism in multiple independent studies. Regions of LCSH are reported when they are greater than 10 Mb. Deletions smaller than 200 kb and duplications smaller than 500 kb are NOT REPORTED, unless they involve regions of the genome with clear clinical significance.

Staining copper in tissues

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%.

Mantle cell lymphoma, breast cancer

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

Normal and abnormal epithelial cells and to determine lineage of poorly differentiated tumors

Variety of epithelium and epithelial malignancies including adenocarcinoma of colon, stomach, pancreas, biliary tract and breast

GI tumors, transitional cell carcinoma, Merkel cell tumors