Diagnosis; Drug Response; Mutation Confirmation; Predictive; Prognostic

Establish or confirm diagnosis

Guidance for management

In hemochromatosis, iron is absorbed from the diet resulting in an accumulation and subsequent deposition in the liver, skin, pancreas, heart, brain, and endocrine organs. The iron deposition leads to oxidative damage and subsequent development of cirrhosis, diabetes, arthropathy, cardiomyopathy, and endocrinopathy. The current commonly implemented genetic test for hemochromatosis … In hemochromatosis, iron is absorbed from the diet resulting in an accumulation and subsequent deposition in the liver, skin, pancreas, heart, brain, and endocrine organs. The iron deposition leads to oxidative damage and subsequent development of cirrhosis, diabetes, arthropathy, cardiomyopathy, and endocrinopathy. The current commonly implemented genetic test for hemochromatosis is derived from the genotype of two common single nucleotide polymorphisms located in the HFE gene (C282Y and H63D). Unfortunately, the HFE genetic test is neither sensitive nor specific as only 75-90% of patients with clinical hemochromatosis test positive, while only 13% of those who test positive will go on to develop iron overload with end organ dysfunction. Substantial genetic and phenotypic heterogeneity exists, and heterozygous and homozygous mutations have been identified in at least 14 different genes leading to iron overload phenotypes. This gene panel tests for genetic mutations associated with: hemochromatosis; juvenile hemochromatosis (type 2A and 2B), hemochromatosis (type 3, and 5), ferroportin disease (type 4), atransferrinemia, familial hypercatabolic hypoproteinemia, aceruloplasminemia, hyperferritinemia-cataract syndrome, dysrethropoietic anemia type I and II, dyserythropoietic anemia type II, sideroblastic anemia hypochromic and microcytic anemia with iron overload, X-linked sideroblastic anemia. View more

All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; … All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual). All exons have >1000x mean read depth coverage, with a minimum 200x coverage at a single nucleotide resolution. This assay meets the sensitivity and specificity of combined Sanger sequencing and MLPA copy number analysis. All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon reques View more

Illumina MiSeq/ NextSeq

Mutations identified are repeated in an independent assay using either Sanger sequence, MLPA, Q-PCR or other.

Tests performed
Entire test performed in-house

This assay meets the sensitivity and specificity of combined Sanger sequencing and MLPA copy number analysis, >99%

Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP

Software used to interpret novel variations Help
SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual with HGMD

Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request