The impact of clinical genome sequencing in a global population with suspected rare genetic disease.

There is mounting evidence of the value of clinical genome sequencing (cGS) in individuals with suspected rare genetic disease (RGD), but cGS performance and impact on clinical care in a diverse population drawn from both high-income countries (HICs) and low- and middle-income countries (LMICs) has not been investigated. The iHope program, a philanthropic cGS initiative, established a network of 24 clinical sites in eight countries through which it provided cGS to individuals with signs or symptoms of an RGD and constrained access to molecular testing. A total of 1,004 individuals (median age, 6.5 years; 53.5% male) with diverse ancestral backgrounds (51.8% non-majority European) were assessed from June 2016 to September 2021. The diagnostic yield of cGS was 41.4% (416/1,004), with individuals from LMIC sites 1.7 times more likely to receive a positive test result compared to HIC sites (LMIC 56.5% [195/345] vs. HIC 33.5% [221/659], OR 2.6, 95% CI 1.9-3.4, p < 0.0001). A change in diagnostic evaluation occurred in 76.9% (514/668) of individuals. Change of management, inclusive of specialty referrals, imaging and testing, therapeutic interventions, and palliative care, was reported in 41.4% (285/694) of individuals, which increased to 69.2% (480/694) when genetic counseling and avoidance of additional testing were also included. Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation (OR 6.1, 95% CI 1.1-∞, p = 0.05) and change of management (OR 0.9, 95% CI 0.5-1.3, p = 0.49). Increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities.

Damaging variants in FOXI3 cause microtia and craniofacial microsomia.

PURPOSE: Craniofacial microsomia (CFM) represents a spectrum of craniofacial malformations, ranging from isolated microtia with or without aural atresia to underdevelopment of the mandible, maxilla, orbit, facial soft tissue, and/or facial nerve. The genetic causes of CFM remain largely unknown. METHODS: We performed genome sequencing and linkage analysis in patients and families with microtia and CFM of unknown genetic etiology. The functional consequences of damaging missense variants were evaluated through expression of wild-type and mutant proteins in vitro. RESULTS: We studied a 5-generation kindred with microtia, identifying a missense variant in FOXI3 (p.Arg236Trp) as the cause of disease (logarithm of the odds = 3.33). We subsequently identified 6 individuals from 3 additional kindreds with microtia-CFM spectrum phenotypes harboring damaging variants in FOXI3, a regulator of ectodermal and neural crest development. Missense variants in the nuclear localization sequence were identified in cases with isolated microtia with aural atresia and found to affect subcellular localization of FOXI3. Loss of function variants were found in patients with microtia and mandibular hypoplasia (CFM), suggesting dosage sensitivity of FOXI3. CONCLUSION: Damaging variants in FOXI3 are the second most frequent genetic cause of CFM, causing 1% of all cases, including 13% of familial cases in our cohort.

Turner syndrome in diverse populations.

Turner syndrome (TS) is a common multiple congenital anomaly syndrome resulting from complete or partial absence of the second X chromosome. In this study, we explore the phenotype of TS in diverse populations using clinical examination and facial analysis technology. Clinical data from 78 individuals and images from 108 individuals with TS from 19 different countries were analyzed. Individuals were grouped into categories of African descent (African), Asian, Latin American, Caucasian (European descent), and Middle Eastern. The most common phenotype features across all population groups were short stature (86%), cubitus valgus (76%), and low posterior hairline 70%. Two facial analysis technology experiments were conducted: TS versus general population and TS versus Noonan syndrome. Across all ethnicities, facial analysis was accurate in diagnosing TS from frontal facial images as measured by the area under the curve (AUC). An AUC of 0.903 (p < .001) was found for TS versus general population controls and 0.925 (p < .001) for TS versus individuals with Noonan syndrome. In summary, we present consistent clinical findings from global populations with TS and additionally demonstrate that facial analysis technology can accurately distinguish TS from the general population and Noonan syndrome.

Novel mutation in ENG gene causing Hereditary Hemorrhagic Telangiectasia in a Peruvian family.

Hereditary Hemorrhagic Telangiectasia (HHT) is a rare disorder of vascular development. Common manifestations include epistaxis, telangiectasias and arteriovenous malformations (AVMs) in multiple organs. Most patients have deletions or missense mutations in the ENG or ACVRL1 gene respectively, significantly affecting endothelium homeostasis. We analyzed the ENG gene in five members of a Peruvian family affected by HHT. One novel mutation was found in exon four of the ENG gene c.408delA, at aminoacid residue 136. This mutation changes the subsequent reading frame producing an early stop at residue 162, preserving only one fourth of the normal protein of 658 aa. This mutation was found in the four affected members of family.

Clinical genome sequencing in patients with suspected rare genetic disease in Peru.

There is limited access to molecular genetic testing in most low- and middle-income countries. The iHope program provides clinical genome sequencing (cGS) to underserved individuals with signs or symptoms of rare genetic diseases and limited or no access to molecular genetic testing. Here we describe the performance and impact of cGS in 247 patients from three clinics in Peru. Although most patients had at least one genetic test prior to cGS (70.9%), the most frequent was karyotyping (53.4%). The diagnostic yield of cGS was 54.3%, with candidate variants reported in an additional 22.3% of patients. Clinical GS results impacted clinician diagnostic evaluation in 85.0% and genetic counseling in 72.1% of cases. Changes in management were reported in 71.3%, inclusive of referrals (64.7%), therapeutics (26.3%), laboratory or physiological testing (25.5%), imaging (19%), and palliative care (17.4%), suggesting that increased availability of genomic testing in Peru would enable improved patient management.

Haploinsufficiency of SF3B2 causes craniofacial microsomia.

Craniofacial microsomia (CFM) is the second most common congenital facial anomaly, yet its genetic etiology remains unknown. We perform whole-exome or genome sequencing of 146 kindreds with sporadic (n = 138) or familial (n = 8) CFM, identifying a highly significant burden of loss of function variants in SF3B2 (P = 3.8 × 10-10), a component of the U2 small nuclear ribonucleoprotein complex, in probands. We describe twenty individuals from seven kindreds harboring de novo or transmitted haploinsufficient variants in SF3B2. Probands display mandibular hypoplasia, microtia, facial and preauricular tags, epibulbar dermoids, lateral oral clefts in addition to skeletal and cardiac abnormalities. Targeted morpholino knockdown of SF3B2 in Xenopus results in disruption of cranial neural crest precursor formation and subsequent craniofacial cartilage defects, supporting a link between spliceosome mutations and impaired neural crest development in congenital craniofacial disease. The results establish haploinsufficient variants in SF3B2 as the most prevalent genetic cause of CFM, explaining ~3% of sporadic and ~25% of familial cases.

New SHH and Known SIX3 Variants in a Series of Latin American Patients with Holoprosencephaly.

Holoprosencephaly (HPE) is the failure of the embryonic forebrain to develop into 2 hemispheres promoting midline cerebral and facial defects. The wide phenotypic variability and causal heterogeneity make genetic counseling difficult. Heterozygous variants with incomplete penetrance and variable expressivity in the SHH, SIX3, ZIC2, and TGIF1 genes explain ∼25% of the known causes of nonchromosomal HPE. We studied these 4 genes and clinically described 27 Latin American families presenting with nonchromosomal HPE. Three new SHH variants and a third known SIX3 likely pathogenic variant found by Sanger sequencing explained 15% of our cases. Genotype-phenotype correlation in these 4 families and published families with identical or similar driver gene, mutated domain, conservation of residue in other species, and the type of variant explain the pathogenicity but not the phenotypic variability. Nine patients, including 2 with SHH pathogenic variants, presented benign variants of the SHH, SIX3, ZIC2, and TGIF1 genes with potential alteration of splicing, a causal proposition in need of further studies. Finding more families with the same SIX3 variant may allow further identification of genetic or environmental modifiers explaining its variable phenotypic expression.

MYT1 role in the microtia-craniofacial microsomia spectrum.

BACKGROUND: Craniofacial microsomia (CFM), also known as the oculo-auriculo-vertebral spectrum, comprises a variable phenotype with the most common features including microtia and mandibular hypoplasia on one or both sides, in addition to lateral oral clefts, epibulbar dermoids, cardiac, vertebral, and renal abnormalities. The etiology of CFM is largely unknown. The MYT1 gene has been reported as a candidate based in mutations found in three unrelated individuals. Additional patients with mutations in this gene are required to establish its causality. We present two individuals with CFM that have rare variants in MYT1 contributing to better understand the genotype and phenotype associated with mutations in this gene. METHODS/RESULTS: We conducted genetic analysis using whole-exome and -genome sequencing in 128 trios with CFM. Two novel MYT1 mutations were identified in two participants. Sanger sequencing was used to confirm these mutations. CONCLUSION: We identified two additional individuals with CFM who carry rare variants in MYT1, further supporting the presumptive role of this gene in the CFM spectrum.

¿Cuál es el rol actual de la toracocentesis en el hidrotórax fetal severo? Presentación de caso

Se llama hidrotórax a una efusión pleural primaria que ocurre durante la vida prenatal (denominado 'quilotórax primario' después del nacimiento). En ciertos casos, esta efusión es severa y produce compresión pulmonar y cardiaca, por lo cual, la mortalidad perinatal sigue siendo alta. Los recién nacidos con hidrotórax requieren, muchas veces, de drenaje, nutrición parenteral total y medicación específica para su recuperación. Sin embargo, las intervenciones prenatales, principalmente con derivaciones toraco-amnióticas, pueden mejorar estos resultados. Reportamos el caso de un feto con hidrotórax severo a quien se le realizó una toracocentesis y revisamos la literatura acerca de su rol en el tratamiento prenatal actual.

Hydrothorax is a primary pleural effusion that occurs during prenatal life (called "primary chylothorax" after birth). In certain cases, this effusion is severe and produces pulmonary and cardiac compression, and perinatal mortality remains high. Newborns with hydrothorax often require drainage, total parenteral nutrition and specific medication for their recovery. However, prenatal interventions, mainly with thoraco-amniotic shunts, can improve these results. We report the case of a fetus with severe hydrothorax who underwent thoracentesis and review the literature on its role in current prenatal management.

Factores asociados a la presencia de fisura labiopalatina en recién nacidos en un hospital peruano de tercer nivel de atención. Un estudio de casos y controles / Factors associated to the occurrence of cleft lip and palate in newborns in a tertiary care Peruvian hospital. A case-control study

RESUMEN Objetivo: identificar los factores asociados a la presencia de fisura labial y/o palatina en recién nacidos en el Hospital Nacional Edgardo Rebagliati Martins, localizado en Lima - Perú, durante el periodo noviembre 2012 - diciembre 2016. Materiales y métodos: estudio observacional, analítico, de casos y controles emparejado, con datos del Estudio Colaborativo Latinoamericano de Malformaciones Congénitas (ECLAMC). Se analizaron 61 casos y 61 controles. La variable dependiente fue la presencia de fisura labial y/o palatina. Se recogieron también variables clínicas, epidemiológicas, obstétricas y prenatales. Resultados: la fisura labiopalatina con extensión completa, en el sexo masculino, fue la forma más frecuente y estuvo presente en 36 neonatos (59%), con cariotipo normal 44 (75,9%) y sin diagnóstico prenatal 40 (65,6%). Las malformaciones observadas con más frecuencia fueron las faciales 27 (44,2%) seguidas de malformaciones cardiacas (29,6%). Se construyó un modelo estadístico mediante análisis multivariado conformado por tres variables: enfermedad crónica durante el embarazo (odds ratio (OR): 3,8; intervalo de confianza al 95% (IC 95%): 1,11 - 13,08), edad materna mayor a 35 años (OR: 6,85; IC 95%: 2,69 - 17,43) y antecedente familiar (OR: 14,5; IC 95%: 1,68 - 125,56). Conclusiones: las enfermedades crónicas en el embarazo, la edad materna avanzada y el antecedente familiar fueron factores que aumentaron la presencia de fisura labial y/o palatina.

ABSTRACT Objective: to identify factors associated to the occurrence of cleft lip and/or palate in newborns in Edgardo Rebagliati-Martins National Hospital in Lima, Peru, during the time period from November 2012 until December 2016. Materials and methods: this is an analytical observational paired case-control study, with data from the Collaborative Latin-American Study of Congenital Malformations. Sixty-one cases and sixty-one controls were analyzed. The dependent variable was the presence of cleft lip and/or palate. Clinical, epidemiological, obstetric, and prenatal variables were also analyzed. Results : cleft lip/palate with complete extension predominantly in males was the most frequent form, and it was present in 36 neonates (59%), 44 of all children in the sample (75.9%) had normal karyotype, and 40 did not have a prenatal diagnosis (65.6%). Associated malformations most frequently observed were 27 facial cases (44.2%), followed by cardiac malformations (29.6%). A statistical model using multivariate analysis was built on, and this comprised three variables: chronic disease during pregnancy (odds ratio (OR): 3.8; 95% confidence interval (CI): 1.11-13.8), maternal age more than 35 years (OR: 6.85; 95% CI: 2.69-17.43), and family history (OR: 14.5; 95% CI: 1.68-125.56). Conclusions : chronic diseases during pregnancy, advanced maternal age, and family history were factors that increased the frequency of cleft lip and/or palate.