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Background Loss-of-Function (LoF) variants in human genes are important due to their impact on clinical phenotypes and frequent occurrence in the genomes of healthy individuals. The association of LoF variants with complex diseases and traits may lead to the discovery and validation of novel therapeutic targets. Current approaches predict high-confidence LoF variants without identifying the specific genes or the number of copies they affect. Moreover, there is a lack of methods for detecting knockout genes caused by compound heterozygous (CH) LoF variants. Results We have developed the Loss-of-Function ToolKit (LoFTK), which allows efficient and automated prediction of LoF variants from genotyped, imputed and sequenced genomes. LoFTK enables the identification of genes that are inactive in one or two copies and provides summary statistics for downstream analyses. LoFTK can identify CH LoF variants, which result in LoF genes with two copies lost. Using data from parents and offspring we show that 96% of CH LoF genes predicted by LoFTK in the offspring have the respective alleles donated by each parent. Conclusions LoFTK is a command-line based tool that provides a reliable computational workflow for predicting LoF variants from genotyped and sequenced genomes, identifying genes that are inactive in 1 or 2 copies. LoFTK is an open software and is freely available to non-commercial users at https://github.com/CirculatoryHealth/LoFTK.

BACKGROUND Kaposi sarcoma (KS) is a complication of KS-associated herpesvirus (KSHV) infection. Other oncogenic viral infections and malignancies are associated with certain HLA alleles and their natural killer (NK) cell immunoglobulin-like receptor (KIR) ligands. We tested whether HLA-KIR influences the risk of KSHV infection or KS. METHODS In population-based case-control studies, we compared HLA class I and KIR gene frequencies in 250 classic (non-AIDS) KS cases, 280 KSHV-seropositive controls, and 576 KSHV-seronegative controls composing discovery and validation cohorts. Logistic regression was used to calculate sex- and age-adjusted odds ratios (ORs) and 95% confidence intervals. RESULTS In both the discovery and validation cohorts, KS was associated with HLA-A*11:01 (adjusted OR for the combined cohorts, 0.4; P = .002) and HLA-C*07:01 (adjusted OR, 1.6; P = .002). Consistent associations across cohorts were also observed with activating KIR3DS1 plus HLA-B Bw4-80I and homozygosity for HLA-C group 1. With KIR3DS1 plus HLA-B Bw4-80I, the KSHV seroprevalence was 40% lower (adjusted OR for the combined cohorts, 0.6; P = .01), but the KS risk was 2-fold higher (adjusted OR, 2.1; P = .002). Similarly, the KSHV seroprevalence was 40% lower (adjusted OR, 0.6; P = .01) but the KS risk 80% higher with HLA-C group 1 homozygosity (adjusted OR, 1.8; P = .005). CONCLUSIONS KIR-mediated NK cell activation may decrease then risk of KSHV infection but enhance KSHV dissemination and progression to KS if infection occurs.

Introducción: Las pérdidas auditivas son heredables en un 50-60% de los casos. Dentro de estas, las sorderas no sindrómicas predominan y se han descrito más de 40 genes asociados. Uno de los más frecuentemente implicados es el gen de Otoferlina (OTO F).Objetivo: Determinar la frecuencia de la mutación p.Q829X en el gen OTO F en 649 individuos colombianos con sordera no sindrómica.Materiales y métodos: Se seleccionó una población de 649 individuos para realizar la búsqueda de la mutación p.Q829X por medio de la técnica PCR-RFLP. Resultados: Se identificaron 12 individuos con la mutación p.Q829X (12/649), que corresponden a una frecuencia del 1,8%.Conclusiones:La mutación p.Q829X es la más frecuente en el gen OTO F, y la tercera luego de las mutaciones S199F y 35delG en el gen GJB2, causantes de sordera en la población analizada. Se observó variabilidad en el grado de pérdida auditiva en los individuos homocigotos para la mutación y presencia de neuropatía auditiva en el 62,5% de estos casos. Introduction:Hearing loss is 50-60% heritable. among this, non-syndromic hearing loss is pre-dominant and more than 40 genes have been re-ported. one of the most frequently involved is otoFgene. Objective:to identify the frequency of muta-tion p.Q829X in otoF gene, in 649 colombian individuals with non-syndromic deafness. Materials and Methods:a total of 649 indi-viduals were selected and screened for p.Q829X mutation using Pcr-rFlP analysis. Results:p.Q829X mutation was identified in 12 deaf individuals (12/649) corresponding to a fre-quency of 1,8%. Conclusions:p.Q829X mutation is the most common in otoF gene, and the third cause after S199F and 35delg mutations in gJB2 gene, of deafness in the analyzed population. Variability is observed in the degree of hearing loss in in-dividuals homozygous for the mutation and au-ditory neuropathy is present in 62,5% of these cases.