Identification of hypopituitarism related variants in argentinean patients by molecular inversion probe sequencing (MIPS), a novel molecular approach for low cost sequencing

MORTENSEN AH; BERGADA I; KITZMAN JO; PEREZ MILLAN MI; MIRANDA LUCAS; KESELMAN A; SEILICOVICH A; MARTI MA; VISHNOPOLSKA SA; BRASLAVSKY D; BELGOROSKY A; CAMPER SA

Mar del Plata

Congreso; LXIII Reunión de la Sociedad Argentina de Investigación Clínica; 2018

Pituitary hormone deficiency occurs ~1:4,000 live births. Over 30 genes have been implicated in isolated and/or combined pituitary hormone deficiency (IGHD/CPHD). Mutations are estimated to account for ~16% of patient cases, thus the majority of familial and sporadic cases have no known genetic origin. We recently implemented a novel and cost-effective approach based on Molecular Inversion Probe Sequencing (MIPS) to identify novel variants and candidate genes in sporadic trios and familial cases of CPHD and IGHD. We captured 693 coding exons of 30 known genes and 37 candidate genes. We captured genomic DNA from 176 pediatric patients from Argentina with CPHD or IGHD and 133 relatives and conducted next generation sequencing. We obtained a 600X average coverage per sample over targeted regions. We discovered 10 likely pathogenic variants; 8 of them are novel. We classified each variant following the ACMG-AMP guidelines, which is so far the most detailed and quantitative system for variant interpretation in genetic testing. We identified heterozygous variants in 6 genes: GH1 (p.Arg209His), GLI2 (p.Leu761Phe, p.Ser1048fs and p.Lys1162Arg), LHX3 (p.Pro187Ser, p.Leu220Met), LHX4 (p.Gln100His, p.Trp204Leu), PNPLA6 (p.Thr1115Pro) and HESX1 (p.Ile26Thr and p.Gln117*). Mutations in PROP1 are the most common known cause of CPHD, accounting for 11% of total cases worldwide. The frequency of PROP1 mutations varies widely by population group, and the rate was previously unknown for Argentina. We found no cases of PROP1 mutations. We are testing the effects of these variants on the activity of the transcription factors in cell culture. Identification of disease causing mutations in CPHD is complicated by phenotypic variation and incomplete penetrance. Identifying potential pathogenic variants will make it feasible to predict clinical outcomes from genetic data, which is necessary for patient diagnosis and prognosis, and for assessing the risk of future affected individuals.