A novel 50-kb deletion in ANOS1 in a large pedigree with isolated central hypogonadism and olfactory dysfunction (Kallmann Syndrome): NGS as a predictive tool of CNVs

CASTRO, SEBASTIÁN; SANSÓ, GABRIELA; BRASLAVSKY, DEBORA; SCAGLIA, PAULA; IZQUIERDO, AGUSTÍN; ESNAOLA AZCOITI, MARÍA; MAIER, MARIANELA; FIGUEROA GACITUA, VERÓNICA; CORREA BRITO LOURDES; BERGADÁ, IGNACIO; REY, RODOLFO A.; ROPELATO, MARÍA GABRIELA; GRINSPON, ROMINA P.

Bogotá

Congreso; XXX Annual Meeting of the Latin American Pediatric Endocrinology Society (SLEP); 2022

Latin American Pediatric Endocrinology Society (SLEP)

Next generation sequencing (NGS) techniques have allowed the identification of causal variants in approximately 30-50% of patients with isolated central hypogonadism. In cases where no clinically relevant sequence variant is found, the presence of copy number variants (CNV) in candidate genes should be investigated.A large pedigree is presented in which the index patient consulted for bilateral cryptorchidism at one year of age. He was lost to follow-up until the age of 16 years when he presented with absence of pubertal signs, anosmia and persistent cryptorchidism. A GnRH infusion test confirmed the diagnosis of central hypogonadism (peak LH: 0.12 IU/l, peak FSH: 0.7 IU/l). His two younger brothers and a first cousin were referred during the period of physiological postnatal activation of the gonadal axis with bilateral cryptorchidism and micropenis. Gonadotrophins, testosterone and anti-müllerian hormone were low, and central hypogonadism was confirmed after a GnRH infusion test at pubertal age. All of them had olfactory disturbance and two of them had renal malformations. Molecular study was performed on the proband's genomic DNA by NGS using the TruSight One capture kit on a NextSeq 500 sequencer. Sequencing results, analysed using a virtual panel of 83 candidate genes, did not reveal any causal single nucleotide variant or small insertion/deletion. However, bioinformatic analysis predicted a deletion of about 50 kb disrupting exons 4 to 6 of ANOS1 (Xp22.31). To confirm predicted deletion, we designed specific oligonucleotides to amplify a DNA fragment containing the deletion breakpoints and flanking regions, followed by Sanger sequencing. This strategy allowed clarifying the deletion spread (49981 bp) and mapping its breakpoints (NC_000023.11:g.8541618_8591598del, NM_000216.4:c.318+51_857-2873del). According to ACMG and ClinGen criteria, this novel deletion was classified as pathogenic. The deletion was confirmed as hemizygous in the index case, his brothers and cousin and heterozygous in his mother and aunt.In conclusion, we describe a novel deletion of approximately 50-kb in ANOS1 responsible for central hypogonadism with olfactory dysfunction in a large pedigree. Bioinformatic algorithms applied on NGS data are able to predict the presence of CNVs and may contribute to unveil the molecular basis of central hypogonadism, leading to benefits for affected families through reverse phenotyping and genetic counselling.