Computational protocol: Analysis of possible genetic risk factors contributing to development of childhood acute lymphoblastic leukaemia in the Latvian population

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Protocol publication

[…] Statistical analysis using the hybrid method for the case-control study and case-parent study was performed using the R program package “Haplin” []. To analyse case-parent trios the family-based association test (FBAT) by the transmission distortion test (TDT) and the haplotype-based TDT were performed, as implemented in the software PLINK 1.07 []. To separately analyse the case-control model the software JavaStat (available online) was used, the Fisher exact test was used for statistical analysis, and a p-value < 0.05 was considered as statistically significant. […]

Pipeline specifications

Software tools Haplin, PLINK
Application GWAS
Organisms Homo sapiens
Diseases Precursor Cell Lymphoblastic Leukemia-Lymphoma