GStream: improving SNP and CNV coverage on genome-wide association studies

PMP22-Related neuropathies and other clinical manifestations in Chinese han patients with charcot-marie-tooth disease type 1

INTRODUCTION

Most cases of Charcot-Marie-Tooth (CMT) disease are caused by mutations in the peripheral myelin protein 22 gene (PMP22), including heterozygous duplications (CMT1A), deletions (HNPP), and point mutations (CMT1E).

METHODS

Single-nucleotide polymorphism (SNP) arrays were used to study PMP22 mutations based on the results of multiplex ligation-dependent probe amplification (MLPA) and polymerase chain reaction-restriction fragment length polymorphism methods in 77 Chinese Han families with CMT1. PMP22 sequencing was performed in MLPA-negative probands. Clinical characteristics were collected for all CMT1A/HNPP probands and their family members.

RESULTS

Twenty-one of 77 CMT1 probands (27.3%) carried duplication/deletion (dup/del) copynumber variants. No point mutations were detected. SNP array and MLPA seem to have similar sensitivity. Fifty-seven patients from 19 CMT1A families had the classical CMT phenotype, except for 1 with concomitant CIDP. Two HNPP probands presented with acute ulnar nerve palsy or recurrent sural nerve palsy, respectively.

CONCLUSIONS

The SNP array has wide coverage, high sensitivity, and high resolution and can be used as a screening tool to detect PMP22 dup/del as shown in this Chinese Han population.

Lack of association between insulin receptor substrate2 rs1805097 polymorphism and the risk of colorectal and breast cancer: a meta-analysis

BACKGROUND

Insulin receptor substrate-2 (IRS-2), a signaling adaptor protein, was involved in two cancer-related pathways (the phosphatidylinositol 3'-kinase (PI3K) and the extracellular signal-regulated kinase (ERK) pathways). Several studies have evaluated the association between IRS2 rs1805097 (G>A) polymorphisms and the risk of colorectal and breast cancer. However, the results were inconsistent.

METHODOLOGY/PRINCIPAL FINDINGS

A meta-analysis of seven published case-control studies (4 studies with 4798 cases and 5478 controls for colorectal cancer and 3 studies with 2108 cases and 2507 controls for breast cancer) were conducted to assess the strength of association using crude odd ratios (ORs) with 95% confidence intervals (CIs). For colorectal cancer, no obvious associations were found for all genetic models (homozygote comparison OR = 0.96, 95%CI 0.85-1.08, Pheterogeneity = 0.97; heterozygote comparison: OR = 0.91, 95%CI 0.73-1.13, Pheterogeneity<0.01; dominant model: OR = 0.92, 95%CI 0.80-1.06, Pheterogeneity = 0.05; recessive model: OR = 1.02, 95%CI 0.91-1.14, Pheterogeneity = 0.60). In the subgroup analysis by ethnicity, control source and consistency of frequency with Hardy-Weinberg equilibrium (HWE), still no significant associations were observed. For breast cancer, also no obvious associations were found for all genetic models (homozygote comparison: OR = 0.95, 95%CI 0.71-1.26, Pheterogeneity = 0.10; heterozygote comparison: OR = 1.00, 95%CI 0.89-1.14, Pheterogeneity = 0.71; dominant model: OR = 0.98, 95%CI 0.87-1.10, Pheterogeneity = 0.55; recessive model: OR = 0.95, 95%CI 0.72-1.25, Pheterogeneity = 0.07). We performed subgroup analyses by sample size and did not find an association.

CONCLUSIONS

This meta-analysis indicated that IRS2 rs1805097 polymorphism was not associated with colorectal and breast cancer risk.