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.

Usefulness of automated image analysis for recognition of the fragile X syndrome gestalt in Congolese subjects.

BACKGROUND: Computer-aided software such as the facial image diagnostic aid (FIDA) and Face2Gene has been developed to perform pattern recognition of facial features with promising clinical results. The aim of this pilot study was to test Face2Gene's recognition performance on Bantu Congolese subjects with Fragile X syndrome (FXS) as compared to Congolese subjects with intellectual disability but without FXS (non-FXS). METHOD: Frontal facial photograph from 156 participants (14 patients with FXS and 142 controls) predominantly young-adults to adults, median age 18.9 age range 4-39yo, were uploaded. Automated face analysis was conducted by using the technology used in proprietary software tools called Face2Gene CLINIC and Face2Gene RESEARCH (version 17.6.2). To estimate the statistical power of the Face2Gene technology in distinguishing affected individuals from controls, a cross validation scheme was used. RESULTS: The similarity seen in the upper facial region (of males and females) is greater than the similarity seen in other parts of the face. Binary comparison of subjects with FXS versus non-FXS and subjects with FXS versus subjects with Down syndrome reveal an area under the curve values of 0.955 (p = 0.002) and 0.986 (p = 0.003). CONCLUSION: The Face2Gene algorithm is separating well between FXS and Non-FXS subjects.

Objective evaluation of facial features in Congolese newborns by facial measurements. The need for population-specific measurements.

The evaluation of dysmorphism is often subjective because many continuous traits are not easily measured or lack normal values. Because many common morphologic profiles vary between populations, population-specific reference ranges of relevant traits are needed. We aim to evaluate the objective assessment of facial dysmorphism in 553 Congolese newborns based on facial measurements. Measurements taken with a ruler were on average larger compared to those with a caliper, but the bias did not depend on the size of the measurement. We therefore introduced a correction factor that allows to use both techniques for facial measurements interchangeably in future studies. The outer canthal distance, palpebral fissure length, and mouth width were significantly larger in Congolese newborns (respectively mean 6.59 [SD 0.48]; mean 2.20 [SD 0.24]; mean 2.78 [SD 0.26]) when compared to references based on European newborns (respectively mean 3.59 [SD 1.76]; mean 4.20 [SD 2.26]; mean 0.47 [SD 1.21]), while the rest of measurements were significantly smaller. The interpupillary distance (IPD) calculated from inner canthal distance and outer canthal distance was not significantly different. We observed a poor agreement between clinical evaluation and measured features (kappa of 0.432). Clinicians were more likely to recognize a face as having wide-spaced eyes when it had been recognized as such during the clinical examination, more than if the child had a high interpupillary distance. This suggests that the measured IPD is not precisely reflecting what is clinically evaluated as wide-spaced eyes.

PERCHING syndrome: Clinical presentation in the first African patient confirmed by clinical whole genome sequencing.

PERCHING syndrome is a rare multisystem developmental disorder caused by autosomal recessive (AR) variants (truncating and missense) in the Kelch-like family member 7 gene (KLHL7). We report the first phenotypic and molecular description of PERCHING syndrome in a patient from Central Africa. The patient presented multiple dysmorphic features in addition to neurological, respiratory, gastroenteric, and dysautonomic disorders. Clinical Whole Genome Sequencing in the proband and his mother identified two novel heterozygous variants in the KLHL7 gene, including a maternally inherited intronic variant (NM_001031710.2:c.793 + 5G > C) classified as Variant of Uncertain Significance and a frameshift stop gain variant (NM_001031710.2:c.944delG; p.Ser315ThrfsTer23) of unknown inheritance classified as likely pathogenic. Although the diagnosis was only evoked after genomic testing, the review of published patients suggests that this disease could be clinically recognizable and maybe considered as an encephalopathy. Our report will allow expanding the phenotypic and molecular spectrum of Perching syndrome.

Increasing African genomic data generation and sharing to resolve rare and undiagnosed diseases in Africa: a call-to-action by the H3Africa rare diseases working group.

The rich and diverse genomics of African populations is significantly underrepresented in reference and in disease-associated databases. This renders interpreting the Next Generation Sequencing (NGS) data and reaching a diagnostic more difficult in Africa and for the African diaspora. It increases chances for false positives with variants being misclassified as pathogenic due to their novelty or rarity. We can increase African genomic data by (1) making consent for sharing aggregate frequency data an essential component of research toolkit; (2) encouraging investigators with African data to share available data through public resources such as gnomAD, AVGD, ClinVar, DECIPHER and to use MatchMaker Exchange; (3) educating African research participants on the meaning and value of sharing aggregate frequency data; and (4) increasing funding to scale-up the production of African genomic data that will be more representative of the geographical and ethno-linguistic variation on the continent. The RDWG of H3Africa is hereby calling to action because this underrepresentation accentuates the health disparities. Applying the NGS to shorten the diagnostic odyssey or to guide therapeutic options for rare diseases will fully work for Africans only when public repositories include sufficient data from African subjects.

The status of emergency obstetric and newborn care in post-conflict eastern DRC: a facility-level cross-sectional study.

BACKGROUND: Pregnancy-related mortality remains persistently higher in post-conflict areas. Part of the blame lies with continued disruption to vital care provision, especially emergency obstetric and newborn care (EmONC). In such settings, assessment of EmONC is essential for data-driven interventions needed to reduce preventable maternal and neonatal mortality. In the North Kivu Province (NKP), the epicentre of armed conflict in eastern Democratic Republic of the Congo (DRC) between 2006 and 2013, the post-conflict status of EmONC is unknown. We assessed the availability, use, and quality of EmONC in 3 health zones (HZs) of the NKP to contribute to informed policy and programming in improving maternal and newborn health (MNH) in the region. METHOD: A cross-sectional survey of all 42 public facilities designated to provide EmONC in 3 purposively selected HZs in the NKP (Goma, Karisimbi, and Rutshuru) was conducted in 2017. Interviews, reviews of maternity ward records, and observations were used to assess the accessibility, use, and quality of EmONC against WHO standards. RESULTS: Only three referral facilities (two faith-based facilities in Goma and the MSF-supported referral hospital of Rutshuru) met the criteria for comprehensive EmONC. None of the health centres qualified as basic EmONC, nor could they offer EmONC services 24 h, 7 days a week (24/7). The number of functioning EmONC per 500,000 population was 1.5. Assisted vaginal delivery was the least performed signal function, followed by parenteral administration of anticonvulsants, mainly due to policy restrictions and lack of demand. The 3 HZs fell short of WHO standards for the use and quality of EmONC. The met need for EmONC was very low and the direct obstetric case fatality rate exceeded the maximum acceptable level. However, the proportion the proportion of births by caesarean section in EmONC facilities was within acceptable range in the HZs of Goma and Rutshuru. Overall, the intrapartum and very early neonatal death rate was 1.5%. CONCLUSION: This study provides grounds for the development of coordinated and evidence-based programming, involving local and external stakeholders, as part of the post-conflict effort to address maternal and neonatal morbidity and mortality in the NKP. Particular attention to basic EmONC is required, focusing on strengthening human resources, equipment, supply chains, and referral capacity, on the one hand, and on tackling residual insecurity that might hinder 24/7 staff availability, on the other.

Clinical presentation and evolution of Xia-Gibbs syndrome due to p.Gly375ArgfsTer3 variant in a patient from DR Congo (Central Africa).

Xia-Gibbs syndrome (XGS) is a very rare genetic condition. The clinical spectrum is very broad and variable. The phenotype and evolution in a Congolese boy with XGS have been reported. At 6 years he had speech delay, drooling, marked hyperactivity, attention deficit, aggressive behavior, and intellectual disability. Dysmorphological evaluation revealed strabismus, mild unilateral ptosis, uplifted ear lobes, flat philtrum, thin upper lip vermillion, high arched palate, and flat feet. Patient-only whole exome sequencing identified a known pathogenic frameshift variant in the AHDC1 gene [NM_001029882.3(AHDC1):c.1122dupC;(p.Gly375ArgfsTer3)]. The clinical follow-up revealed the deterioration of his fine motor skills and significant cerebellar phenotype including tremor, pes cavus, and gait instability at the age of 12 years. This patient was compared with three previously reported patients with the same variant but did not identify a consistent pattern in the evolution of symptoms with age.

Dysmorphism and major anomalies are a main predictor of survival in newborns admitted to the neonatal intensive care unit in the Democratic Republic of Congo.

In Central-Africa, neonatal infections, asphyxia and prematurity are main reasons for admission to the neonatal intensive care unit and major determinants of newborn survival. Also, the outcome of newborns with congenital anomalies is expected to be poor, due to a lack of state-of-the art care. We conducted a study of 102 newborns recruited in the Neonatal Intensive Care Unit (NICU) at the University Hospitals of Kinshasa, DR Congo, to assess the impact of congenital anomalies. The presence of a major anomaly was associated with a hazard ratio of death of 13.2 (95%CI: 3.7-46.7, p < .001). In addition, the presence of three or more minor anomalies was associated with a 4.5-fold increased risk of death (95%CI: 1.1-18.6, p = .04). We conclude that like major anomalies, the presence of three or more minor anomalies should also be given particular attention and that the evaluation of dysmorphism should be promoted in NICU.

Phenotype and growth in Sotos syndrome patient from DR Congo (Central Africa).

Sotos syndrome is a widely studied overgrowth syndrome. Clinical presentation includes excessive growth during childhood, macrocephaly, learning difficulties of various degrees, variable minor features, and distinctive facial gestalt. We provide in this report the first phenotypic and growth description of Sotos syndrome in a patient from Central Africa. At 6 month the patient exhibited axial hypotonia, delayed speech development and dysmorphism including long face, sparse eyebrows, hypertelorism, malar hypoplasia and dark flushing, short philtrum, depressed nasal root, anteverted nares, thick upper and lower lip vermilions, macroglossia, prominent forehead, large and peculiar ears, wide intermammillary distance, deep palmar creases, dysplastic finger nails, partial syndactyly of toes, broad, and overlapping hallux. At 19 months, malar flushing became reddish and a retraction of the middle of the lower lip was observed, resembling a bifid lip. He retained the same clinical features at 31 months. Head circumference, weight, and height where within normal ranges at birth but became all above 97th centiles at 4 months. The height velocity evolved in three phases starting with a very fast growth from birth to 6 months (54 cm/year), then a fast phase from 6 to 16 months (18 cm/year) and a slow phase from 16 to 31 months (4.8 cm/year). Conversely, the patient exhibited an acceleration of weight after the first year of life. Our patient exhibited very prominent lips and deep philtrum, which are common facial traits in African individuals. The current report shows an admixture of ethnic-specific features with syndrome-specific features in an African patient.

Morphological characterization of newborns in Kinshasa, DR Congo: Common variants, minor, and major anomalies.

The evaluation of minor physical variation is crucial in a dysmorphological examination. Currently, data on the spectrum and incidence of minor physical variants in Central African newborns is lacking. We therefore conducted a cross-sectional descriptive study of 722 newborns recruited within the first 24 hr of life, in two large maternities in Kinshasa, DR Congo. Minor anomalies were defined according to the series of articles in AJMG Part A and coded as human phenotype ontology terms. A total of 97 different morphological variants were recorded of which 13 were common. About 34.8% of the newborn carried one minor anomaly, 11.6% had two, and 4.3% had three minor anomalies. No gender differences were observed, but the incidence of specific anomalies appeared to vary with the geographical origin of parents within the DR Congo. The results of this study will aid clinicians to interpret morphological variation in Central African newborns.

A comprehensive clinical and genetic study in 127 patients with ID in Kinshasa, DR Congo.

Pathogenic variants account for 4 to 41% of patients with intellectual disability (ID) or developmental delay (DD). In Sub-Saharan Africa, the prevalence of ID is thought to be higher, but data in Central Africa are limited to some case reports. In addition, clinical descriptions of some syndromes are not available for this population. This study aimed at providing an estimate for the fraction of ID/DD for which an underlying etiological genetic cause may be elucidated and provide insights into their clinical presentation in special institutions in a Central African country. A total of 127 patients (33 females and 94 males, mean age 10.03 ± 4.68 years), were recruited from six institutions across Kinshasa. A clinical diagnosis was achieved in 44 but molecular confirmation was achieved in 21 of the 22 patients with expected genetic defect (95% clinical sensitivity). Identified diseases included Down syndrome (15%), submicroscopic copy number variants (9%), aminoacylase deficiency (0.8%), Partington syndrome in one patient (0.8%) and his similarly affected brother, X-linked syndromic Mental Retardation type 33 (0.8%), and two conditions without clear underlying molecular genetic etiologies (Oculo-Auriculo-Vertebral and Amniotic Bands Sequence). We have shown that genetic etiologies, similar to those reported in Caucasian subjects, are a common etiologic cause of ID in African patients from Africa. We have confirmed the diagnostic utility of clinical characterization prior to genetic testing. Finally, our clinical descriptions provide insights into the presentation of these genetic diseases in African patients.

Williams-Beuren syndrome: pitfalls for diagnosis in limited resources setting.

Patients with Williams-Beuren Syndrome can be recognized clinically, given the characteristic dysmorphism, intellectual disability, and behavior. We report on a Congolese boy with typical WBS facial characteristics. He suffered meningitis and coma at the age of 2 years then subsequently presented with profound intellectual disability and atypical behavior. The WBS was only made at age 8.2 years and confirmed with FISH testing and microarray-CGH. The present report aims to warn clinicians that infections may associate and/or modify a genetic disease as this may be observed in developing countries given the prevalence of infectious diseases.

Skinfold over toenail is pathognomonic for the popliteal pterygium syndrome in a Congolese family with large intrafamilial variability.

KEY CLINICAL MESSAGE: We report on three related Congolese popliteal pterygium syndrome (PPS) patients concordant only for the skinfold over the toenail. Mutation analysis revealed that the three affected individuals carried a heterozygous missense mutation in the Exon 4, NM_006147.2:c.250C>T; p.Arg84Cys. This is the first molecularly confirmed PPS family from central Africa.

A novel heterozygous mutation of three consecutive nucleotides causing Apert syndrome in a Congolese family.

Apert syndrome (OMIM 101200) is a rare genetic condition characterized by craniosynostosis and syndactyly of hands and feet with clinical variability. Two single nucleotides mutations in the linker region between the immunoglobulin-like domains II and IIIa of the ectodomainin the Fibroblast Growth Factor Receptor 2 gene (FGFR2, OMIM 176943) are responsible of the vast majority of cases: c.755C > G; p.Ser252Trp (65%) and c.758C > G; p.Pro253Arg (34%. Three exceptional cases carry multiple substitutions of adjacent nucleotides in the linker region. Here we present a Congolese male patient and his mother, both affected with Apert syndrome of variable severity, carrying a previously undescribed heterozygous mutation of three consecutive nucleotides (c.756_758delGCCinsCTT) in the IgII-IgIIIa linker region. This is the fourth live-born patient to carry a multiple nucleotide substitution in the linker region and is the second alternative amino acid substitutions of the Pro253. Remarkably, this novel mutation was detected in the first Central African patient ever to be tested molecularly for the Apert syndrome. To discriminate between a hitherto unreported mutation and an ethnic specific polymorphism, we tested 105 Congolese controls, and no variation was detected.

X-linked adrenal hypoplasia congenita: a novel DAX1 missense mutation and challenges for clinical diagnosis in Africa.

Adrenal hypoplasia congenita (AHC) is a rare disease. The X-linked form of AHC is caused by deletions or mutations in DAX1 gene and has a variable clinical presentation. To date, no data on X-linked AHC in central Africa are available. Here, we report a Congolese pedigree with several cases of unexplained deaths of male infants. A careful analysis of the pedigree of this family lead to the recognition of an X-linked inheritance pattern, with subsequent confirmation in a female heterozygous carrier of a DAX1 missense mutation c.1274G>T, (p.Arg425Ile).The diagnosis of this condition remains challenging in a developing country, since the manifestations of AHC overlap with those of the much more frequently occurring infections; darkening of the skin is difficult to evaluate and there is a lack of access to routine endocrinological testing. The diagnosis was eventually made based on the family pedigree, evoking an X-linked inheritance pattern. This illustrates the necessity for medical and clinical genetics to be part of the curriculum of medical school in developing countries.