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BACKGROUND: Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS: In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS: Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS: Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
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Exoma , Padrões de Herança , Recém-Nascido , Humanos , Genes Recessivos , Mutação , Sequenciamento do Exoma , Linhagem , Proteínas do Olho/genética , Proteínas de Membrana/genética , Proteínas Nucleares/genética , Proteínas Serina-Treonina Quinases/genética , Peptídeos e Proteínas de Sinalização Intracelular/genéticaRESUMO
INTRODUCTION: Misoprostol is widely used for medication abortion and postpartum hemorrhage. However, it has been associated with the adverse effect of fever, which can pose challenges in management and potentially contribute to unnecessary antibiotic use. The incidence of misoprostol-induced fever in the context of medical abortion has not been extensively studied. METHODS: This retrospective cohort study aimed to determine the incidence of fever following misoprostol administration at a tertiary care hospital in Saudi Arabia. The study included female patients who received misoprostol for pregnancy termination or management of missed or incomplete abortion between January 2017 and December 2019. Data on demographics, misoprostol dosage and route, fever characteristics, outcome of abortion, and antibiotic use were collected. Statistical analysis was preformed using appropriate tests. RESULTS: A total of 213 patients were included in the study. The incidence of fever post-misoprostol administration was 8%. Patients who developed fever had a higher gestational age and received higher doses of misoprostol. However, no significant associations were found between other patient variables and fever incidence. Antibiotic therapy was administered to a almost half of the patients who developed fever post-misoprostol but was determined to be unnecessary in all cases. CONCLUSION: This study contributes to the understanding of misoprostol-induced fever in the context of medical abortion. Further research is needed to explore strategies for reducing unnecessary antibiotic use in this population.
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PurposeThe application of genomic sequencing to investigate unexplained death during early human development, a form of lethality likely enriched for severe Mendelian disorders, has been limited.MethodsIn this study, we employed exome sequencing as a molecular autopsy tool in a cohort of 44 families with at least one death or lethal fetal malformation at any stage of in utero development. Where no DNA was available from the fetus, we performed molecular autopsy by proxy, i.e., through parental testing.ResultsPathogenic or likely pathogenic variants were identified in 22 families (50%), and variants of unknown significance were identified in further 15 families (34%). These variants were in genes known to cause embryonic or perinatal lethality (ALPL, GUSB, SLC17A5, MRPS16, THSD1, PIEZO1, and CTSA), genes known to cause Mendelian phenotypes that do not typically include embryonic lethality (INVS, FKTN, MYBPC3, COL11A2, KRIT1, ASCC1, NEB, LZTR1, TTC21B, AGT, KLHL41, GFPT1, and WDR81) and genes with no established links to human disease that we propose as novel candidates supported by embryonic lethality of their orthologs or other lines of evidence (MS4A7, SERPINA11, FCRL4, MYBPHL, PRPF19, VPS13D, KIAA1109, MOCS3, SVOPL, FEN1, HSPB11, KIF19, and EXOC3L2).ConclusionOur results suggest that molecular autopsy in pregnancy losses is a practical and high-yield alternative to traditional autopsy, and an opportunity for bringing precision medicine to the clinical practice of perinatology.
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Autopsia , Técnicas de Diagnóstico Molecular , Autopsia/métodos , Causas de Morte , Feminino , Genes Letais , Estudos de Associação Genética , Doenças Genéticas Inatas/diagnóstico , Doenças Genéticas Inatas/genética , Predisposição Genética para Doença , Humanos , Medicina de Precisão , Gravidez , Diagnóstico Pré-Natal , Sequenciamento do Exoma , Fluxo de TrabalhoRESUMO
Meckel-Gruber syndrome (MKS) is a perinatally lethal disorder characterized by the triad of occipital encephalocele, polydactyly and polycystic kidneys. Typical of other disorders related to defective primary cilium (ciliopathies), MKS is genetically heterogeneous with mutations in a dozen genes to date known to cause the disease. In an ongoing effort to characterize MKS clinically and genetically, we implemented a gene panel and next-generation sequencing approach to identify the causal mutation in 25 MKS families. Of the three families that did not harbor an identifiable causal mutation by this approach, two mapped to a novel disease locus in which whole-exome sequencing revealed the likely causal mutation as a homozygous splicing variant in TMEM107, which we confirm leads to aberrant splicing and nonsense-mediated decay. TMEM107 had been independently identified in two mouse models as a cilia-related protein and mutant mice display typical ciliopathy phenotypes. Our analysis of patient fibroblasts shows marked ciliogenesis defect with an accompanying perturbation of sonic hedgehog signaling, highly concordant with the cellular phenotype in Tmem107 mutants. This study shows that known MKS loci account for the overwhelming majority of MKS cases but additional loci exist including MKS13 caused by TMEM107 mutation.
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Transtornos da Motilidade Ciliar/genética , Encefalocele/genética , Loci Gênicos , Proteínas de Membrana/genética , Mutação , Doenças Renais Policísticas/genética , Alelos , Cílios/genética , Cílios/metabolismo , Transtornos da Motilidade Ciliar/diagnóstico , Transtornos da Motilidade Ciliar/metabolismo , Consanguinidade , Análise Mutacional de DNA , Encefalocele/diagnóstico , Encefalocele/metabolismo , Feminino , Heterogeneidade Genética , Genótipo , Proteínas Hedgehog/metabolismo , Humanos , Masculino , Linhagem , Doenças Renais Policísticas/diagnóstico , Doenças Renais Policísticas/metabolismo , Retinose Pigmentar , Transdução de SinaisRESUMO
BACKGROUND: Identifying genetic variants that lead to discernible phenotypes is the core of Mendelian genetics. An approach that considers embryonic lethality as a bona fide Mendelian phenotype has the potential to reveal novel genetic causes, which will further our understanding of early human development at a molecular level. Consanguineous families in which embryonic lethality segregates as a recessive Mendelian phenotype offer a unique opportunity for high throughput novel gene discovery as has been established for other recessive postnatal phenotypes. RESULTS: We have studied 24 eligible families using autozygosity mapping and whole-exome sequencing. In addition to revealing mutations in genes previously linked to embryonic lethality in severe cases, our approach revealed seven novel candidate genes (THSD1, PIGC, UBN1, MYOM1, DNAH14, GALNT14, and FZD6). A founder mutation in one of these genes, THSD1, which has been linked to vascular permeability, accounted for embryonic lethality in three of the study families. Unlike the other six candidate genes, we were able to identify a second mutation in THSD1 in a family with a less severe phenotype consisting of hydrops fetalis and persistent postnatal edema, which provides further support for the proposed link between this gene and embryonic lethality. CONCLUSIONS: Our study represents an important step towards the systematic analysis of "embryonic lethal genes" in humans.
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Genes Letais , Mapeamento Cromossômico , Consanguinidade , Embrião de Mamíferos , Exoma , Família , Homozigoto , Humanos , Mutação , Linhagem , Análise de Sequência de DNARESUMO
OBJECTIVE: To ascertain the incidence, and describe the various forms of neural tube defects (NTDs) due to genetic, chromosomal, and syndromic causes. METHODS: We carried out a retrospective analysis of data retrieved from the medical records of newborn infants admitted to the Neonatal Intensive Care Unit with NTDs and their mothers spanning 14 years (1996-2009) at the Security Forces Hospital, Riyadh, Saudi Arabia. The cases were ascertained by a perinatologist, neonatologist, geneticist, radiologist, and neurologist. The literature was reviewed via a MEDLINE search. Only liveborn babies were included. Permission from the Educational Committee at the Security Forces Hospital was obtained prior to the collection of data. RESULTS: Out of 103 infants with NTDs admitted during this period, 20 (19.4%) were found to have an underlying genetic syndromic, chromosomal and/or other anomalies. There were 5 cases of Meckel-Gruber syndrome, 2 Joubert syndrome, one Waardenburg syndrome, one Walker-Warburg syndrome, 2 chromosomal disorders, 2 caudal regression, one amniotic band disruption sequence, one associated with omphalocele, one with diaphragmatic hernia, and 4 with multiple congenital anomalies. CONCLUSION: There is a high rate of underlying genetic syndromic and/or chromosomal causes of NTDs in the Saudi Arabian population due to the high consanguinity rate. Identification of such association can lead to more accurate provisions of genetic counseling to the family including preimplantation genetic diagnosis or early termination of pregnancies associated with lethal conditions.
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Aberrações Cromossômicas , Defeitos do Tubo Neural/genética , Transtornos da Motilidade Ciliar/genética , Consanguinidade , Encefalocele/genética , Feminino , Humanos , Recém-Nascido , Masculino , Doenças Renais Policísticas/genética , Retinose Pigmentar , Estudos Retrospectivos , SíndromeRESUMO
BACKGROUND: Meckel-Gruber syndrome (MKS) is a genetically heterogeneous severe ciliopathy characterised by early lethality, occipital encephalocele, polydactyly, and polycystic kidney disease. PURPOSE: To report genetic analysis results in two families in which all known MKS diseases genes have been excluded. METHODS: In two consanguineous families with classical MKS in which autozygome-guided sequencing of previously reported MKS genes was negative, we performed exome sequencing followed by autozygome filtration. RESULTS: We identified one novel splicing mutation in TMEM231, which led to complete degradation of the mutant transcript in one family, and a novel missense mutation in the other, both in the homozygous state. CONCLUSIONS: TMEM231 represents a novel MKS locus. The very recent identification of TMEM231 mutations in Joubert syndrome supports the growing appreciation of the overlap in the molecular pathogenesis between these two ciliopathies.
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Transtornos da Motilidade Ciliar/genética , Encefalocele/genética , Proteínas de Membrana/genética , Mutação de Sentido Incorreto , Doenças Renais Policísticas/genética , Aborto Espontâneo , Sequência de Aminoácidos , Consanguinidade , Feminino , Humanos , Masculino , Dados de Sequência Molecular , Linhagem , Gravidez , Retinose Pigmentar , Alinhamento de SequênciaRESUMO
Meckel-Gruber syndrome (MKS, OMIM #249000) is a multiple congenital malformation syndrome that represents the severe end of the ciliopathy phenotypic spectrum. Despite the relatively common occurrence of this syndrome among Arabs, little is known about its genetic architecture in this population. This is a series of 18 Arab families with MKS, who were evaluated clinically and studied using autozygome-guided mutation analysis and exome sequencing. We show that autozygome-guided candidate gene analysis identified the underlying mutation in the majority (n=12, 71%). Exome sequencing revealed a likely pathogenic mutation in three novel candidate MKS disease genes. These include C5orf42, Ellis-van-Creveld disease gene EVC2 and SEC8 (also known as EXOC4), which encodes an exocyst protein with an established role in ciliogenesis. This is the largest and most comprehensive genomic study on MKS in Arabs and the results, in addition to revealing genetic and allelic heterogeneity, suggest that previously reported disease genes and the novel candidates uncovered by this study account for the overwhelming majority of MKS patients in our population.