Contribution of SLC22A12 on hypouricemia and its clinical significance for screening purposes

Abstract Differentiating between inherited renal hypouricemia and transient hypouricemic status is challenging. Here, we aimed to describe the genetic background of hypouricemia patients using whole-exome sequencing (WES) and assess the feasibility for genetic diagnosis using two founder variants in primary screening. We selected all cases (N = 31) with extreme hypouricemia (<1.3 mg/dl) from a Korean urban cohort of 179,381 subjects without underlying conditions. WES and corresponding downstream analyses were performed for the discovery of rare causal variants for hypouricemia. Two known recessive variants within SLC22A12 (p.Trp258*, pArg90His) were identified in 24 out of 31 subjects (77.4%). In an independent cohort, we identified 50 individuals with hypouricemia and genotyped the p.Trp258* and p.Arg90His variants; 47 of the 50 (94%) hypouricemia cases were explained by only two mutations. Four novel coding variants in SLC22A12, p.Asn136Lys, p.Thr225Lys, p.Arg284Gln, and p.Glu429Lys, were additionally identified. In silico studies predict these as pathogenic variants. This is the first study to show the value of genetic diagnostic screening for hypouricemia in the clinical setting. Screening of just two ethnic-specific variants (p.Trp258* and p.Arg90His) identified 87.7% (71/81) of Korean patients with monogenic hypouricemia. Early genetic identification of constitutive hypouricemia may prevent acute kidney injury by avoidance of dehydration and excessive exercise.

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A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families

Human Molecular Genetics ◽

10.1093/hmg/ddaa016 ◽

2020 ◽

Vol 29 (6) ◽

pp. 967-979 ◽

Cited By ~ 6

Author(s):

Revital Bronstein ◽

Elizabeth E Capowski ◽

Sudeep Mehrotra ◽

Alex D Jansen ◽

Daniel Navarro-Gomez ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Diagnosis ◽

Genetic Diagnostics ◽

Whole Genome ◽

Unique Challenge ◽

Coding Regions ◽

Pathogenic Variants ◽

Number Of Patients ◽

Coding Variants

Abstract Inherited retinal degenerations (IRDs) are at the focus of current genetic therapeutic advancements. For a genetic treatment such as gene therapy to be successful, an accurate genetic diagnostic is required. Genetic diagnostics relies on the assessment of the probability that a given DNA variant is pathogenic. Non-coding variants present a unique challenge for such assessments as compared to coding variants. For one, non-coding variants are present at much higher number in the genome than coding variants. In addition, our understanding of the rules that govern the non-coding regions of the genome is less complete than our understanding of the coding regions. Methods that allow for both the identification of candidate non-coding pathogenic variants and their functional validation may help overcome these caveats allowing for a greater number of patients to benefit from advancements in genetic therapeutics. We present here an unbiased approach combining whole genome sequencing (WGS) with patient-induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs) transcriptome analysis. With this approach, we identified and functionally validated a novel pathogenic non-coding variant in a small family with a previously unresolved genetic diagnosis.

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Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses

10.1101/2020.08.28.20180414 ◽

2020 ◽

Author(s):

Alison R Barton ◽

Maxwell A Sherman ◽

Ronen E. Mukamel ◽

Po-Ru Loh

Keyword(s):

Fine Mapping ◽

Association Studies ◽

Uk Biobank ◽

Allelic Series ◽

Whole Exome ◽

Causal Variants ◽

Collagen Genes ◽

Coding Variants

Exome association studies to date have generally been underpowered to systematically evaluate the phenotypic impact of very rare coding variants. We leveraged extensive haplotype sharing between 49,960 exome-sequenced UK Biobank participants and the remainder of the cohort (total N~500K) to impute exome-wide variants at high accuracy (R2>0.5) down to minor allele frequency (MAF) ~0.00005. Association and fine-mapping analyses of 54 quantitative traits identified 1,189 significant associations (P<5 x 10-8) involving 675 distinct rare protein-altering variants (MAF<0.01) that passed stringent filters for likely causality; 600 of the 675 variants (89%) were not present in the NHGRI-EBI GWAS Catalog. We replicated the effect directions of 28 of 28 height-associated variants genotyped in previous exome array studies, including missense variants in newly-associated collagen genes COL16A1 and COL11A2. Across all traits, 49% of associations (578/1,189) occurred in genes with two or more hits; follow-up analyses of these genes identified long allelic series containing up to 45 distinct likely-causal variants within the same gene (on average exhibiting 93%-concordant effect directions). In particular, 24 rare coding variants in IFRD2 independently associated with reticulocyte indices, suggesting an important role of IFRD2 in red blood cell development, and 11 rare coding variants in NPR2 (a gene previously implicated in Mendelian skeletal disorders) exhibited intermediate-to-strong effects on height (0.18-1.09 s.d.). Our results demonstrate the utility of within-cohort imputation in population-scale GWAS cohorts, provide a catalog of likely-causal, large-effect coding variant associations, and foreshadow the insights that will be revealed as genetic biobank studies continue to grow.

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Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases

npj Genomic Medicine ◽

10.1038/s41525-021-00261-1 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Zeinab Fadaie ◽

Laura Whelan ◽

Tamar Ben-Yosef ◽

Adrian Dockery ◽

Zelia Corradi ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rare Variants ◽

Genetic Diagnosis ◽

Whole Genome ◽

Retinal Diseases ◽

Structural Variants ◽

Pathogenic Variants ◽

Coding Variants

AbstractInherited retinal diseases (IRDs) are a major cause of visual impairment. These clinically heterogeneous disorders are caused by pathogenic variants in more than 270 genes. As 30–40% of cases remain genetically unexplained following conventional genetic testing, we aimed to obtain a genetic diagnosis in an IRD cohort in which the genetic cause was not found using whole-exome sequencing or targeted capture sequencing. We performed whole-genome sequencing (WGS) to identify causative variants in 100 unresolved cases. After initial prioritization, we performed an in-depth interrogation of all noncoding and structural variants in genes when one candidate variant was detected. In addition, functional analysis of putative splice-altering variants was performed using in vitro splice assays. We identified the genetic cause of the disease in 24 patients. Causative coding variants were observed in genes such as ATXN7, CEP78, EYS, FAM161A, and HGSNAT. Gene disrupting structural variants were also detected in ATXN7, PRPF31, and RPGRIP1. In 14 monoallelic cases, we prioritized candidate noncanonical splice sites or deep-intronic variants that were predicted to disrupt the splicing process based on in silico analyses. Of these, seven cases were resolved as they carried pathogenic splice defects. WGS is a powerful tool to identify causative variants residing outside coding regions or heterozygous structural variants. This approach was most efficient in cases with a distinct clinical diagnosis. In addition, in vitro splice assays provide important evidence of the pathogenicity of rare variants.

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Identification of potential causal variants for premature ovarian failure by whole exome sequencing

BMC Medical Genomics ◽

10.1186/s12920-020-00813-x ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Haengun Jin ◽

JuWon Ahn ◽

YoungJoon Park ◽

JeongMin Sim ◽

Han Sung Park ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Premature Ovarian Failure ◽

Ovarian Failure ◽

Reproductive Age ◽

Bioinformatics Analyses ◽

Korean Patients ◽

Pathogenic Variants ◽

Whole Exome ◽

Causal Variants

Abstract Background Premature ovarian failure (POF) is a highly heterogeneous disorder that occurs in 1% of women of reproductive age. Very few causative genes and variants contributing to POF have been detected, and the disease remains incompletely understood. In this study, we used whole exome sequencing (WES) to identify potential causal variants leading to POF. Methods WES was conducted to identify variants in 34 Korean patients with POF, alongside 10 normal controls. Detected variants were filtered using a range of characterized bioinformatics analyses, and the machine learning tools, CADD and VEST, were used to predict pathogenic variants that could cause disease. VarSome was used for a comprehensive interpretation of the variants. Potential causal variants finally screened by these analyses were confirmed using Sanger sequencing. Results We identified nine potential causative variants in genes previously associated with POF in 8 of 34 (24%) Korean patients by WES variant analysis. These potentially pathogenic variants included mutations in the MCM8, MCM9, and HFM1 genes, which are involved in homologous recombination, DNA repair, and meiosis, and are established as causing POF. Using a combination of CADD and VEST, 72 coding variants were also identified in 72 genes, including ADAMTSL1 and FER1L6, which have plausible functional links to POF. Conclusions WES is a useful tool to detect genetic variants that cause POF. Accumulation and systematic management of data from a number of WES studies in specialized groups of patients with POF (family data, severe case populations) are needed to better comprehend the genetic landscape underlying POF.

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B.06 Whole exome sequencing in genetic ataxias associated with cerebellar atrophy: the Canadian experience

Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques ◽

10.1017/cjn.2019.95 ◽

2019 ◽

Vol 46 (s1) ◽

pp. S11

Author(s):

L Gauquelin ◽

T Hartley ◽

M Tarnopolsky ◽

DA Dyment ◽

B Brais ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Diagnostic Yield ◽

Genetic Diseases ◽

Genetic Diagnosis ◽

Cerebellar Atrophy ◽

Clinical Findings ◽

Disease Genes ◽

Pathogenic Variants ◽

Whole Exome

Background: Cerebellar atrophy is characterized by loss of cerebellar tissue, with evidence on brain imaging of enlarged interfolial spaces compared to the foliae. Genetic ataxias associated with cerebellar atrophy are a heterogeneous group of disorders. We investigated the prevalence in Canada and the diagnostic yield of whole exome sequencing (WES) for this group of conditions. Methods: Between 2011 and 2017, WES was performed in 91 participants with cerebellar atrophy as part of one of two national research programs, Finding of Rare Genetic Disease Genes (FORGE) or Enhanced Care for Rare Genetic Diseases in Canada (Care4Rare). Results: A genetic diagnosis was established in 58% of cases (53/91). Pathogenic variants were found in 24 known genes, providing a diagnosis for 46/53 participants (87%), and in four novel genes, accounting for 7/53 cases (13%). 38/91 cases (42%) remained unsolved. The most common diagnoses were channelopathies in 12/53 patients (23%) and mitochondrial disorders in 9/53 (17%). Inheritance was autosomal recessive in the majority of cases. Additional clinical findings provided useful clues to some of the diagnoses. Conclusions: This is the first report on the prevalence of genetic ataxias associated with cerebellar atrophy in Canada, and the utility of WES for this group of conditions.

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Identification of SOFT syndrome caused by a pathogenic homozygous splicing variant of POC1A: a case report

BMC Medical Genomics ◽

10.1186/s12920-021-01055-1 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Guoqiang Li ◽

Guoying Chang ◽

Chen Wang ◽

Tingting Yu ◽

Niu Li ◽

...

Keyword(s):

Insulin Resistance ◽

Short Stature ◽

Genetic Diagnosis ◽

Facial Dysmorphism ◽

Syndrome Patient ◽

Triangular Face ◽

Splicing Variant ◽

Aberrant Transcript ◽

Pathogenic Variants ◽

Whole Exome

Abstract Background Pathogenic variants in POC1A led to SOFT syndrome and variant POC1A-related (vPOC1A) syndrome. SOFT syndrome is a rare primordial dwarfism condition characterized by short stature, onychodysplasia, facial dysmorphism and hypotrichosis.The main clinical differences between SOFT and vPOC1A syndrome include dyslipidemia with insulin resistance and acanthosis nigricans. To our knowledge, this is the first report of a SOFT syndrome patient diagnosed with a homozygous splicing variant, which could help to extend our understanding of the genotypic and phenotypic information of the disease. Case presentation We reported a seven-year-old boy with SOFT syndrome. The patient presented symmetrical short stature and facial features, including prominent forehead, inverted triangular face, epicanthal fold, small teeth and enlarged ears. Laboratory tests displayed mild insulin resistance. Whole-exome sequencing (WES) led to the identification of a homozygous splicing variant (c.981+1G>A) in POC1A gene of the patient, which was inherited from his heterozygous parents confirmed by Sanger sequencing. Further transcriptional experiments of the splicing variant revealed aberrant percentage of exon 9 skipping transcripts. Conclusions This is the firstly reported case of a SOFT syndrome patient with a novel homozygous splicing variant and detailed delineation of the aberrant transcript in proband and carrier of the variant in Chinese. Our study enriched mutational spectrum of POC1A which could help in further genetic diagnosis and counselling of SOFT syndrome patients.

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High-Throughput Sequencing to Identify Mutations Associated with Retinal Dystrophies

Genes ◽

10.3390/genes12081269 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1269

Author(s):

Fei Song ◽

Marta Owczarek-Lipska ◽

Tim Ahmels ◽

Marius Book ◽

Sabine Aisenbrey ◽

...

Keyword(s):

High Throughput Sequencing ◽

Genetic Diagnosis ◽

Clinical Manifestations ◽

Sequence Variants ◽

Pathogenic Variants ◽

Retinal Dystrophies ◽

Whole Exome ◽

Uncertain Significance ◽

Disease Associated Genes ◽

Intronic Variants

Retinal dystrophies (RD) are clinically and genetically heterogenous disorders showing mutations in over 270 disease-associated genes. Several millions of people worldwide are affected with different types of RD. Studying the relevance of disease-associated sequence alterations will assist in understanding disorders and may lead to the development of therapeutic approaches. Here, we established a whole exome sequencing (WES) pipeline to rapidly identify disease-associated mutations in patients. Sanger sequencing was applied to identify deep-intronic variants and to verify the co-segregation of WES results within families. We analyzed 26 unrelated patients with different syndromic and non-syndromic clinical manifestations of RD. All patients underwent ophthalmic examinations. We identified nine novel disease-associated sequence variants among 37 variants identified in total. The sequence variants located to 17 different genes. Interestingly, two cases presenting with Stargardt disease carried deep-intronic variants in ABCA4. We have classified 21 variants as pathogenic variants, 4 as benign/likely benign variants, and 12 as variants of uncertain significance. This study highlights the importance of WES-based mutation analyses in RD patients supporting clinical decisions, broadly based genetic diagnosis and support genetic counselling. It is essential for any genetic therapy to expand the mutation spectrum, understand the genes’ function, and correlate phenotypes with genotypes.

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Genomic profiling of 553 uncharacterized neurodevelopment patients reveals a high proportion of recessive pathogenic variant carriers in an outbred population

10.1101/675868 ◽

2019 ◽

Author(s):

Youngha Lee ◽

Soojin Park ◽

Jin Sook Lee ◽

Soo Yeon Kim ◽

Jaeso Cho ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Genetic Diagnosis ◽

Pathogenic Variant ◽

Mendelian Disease ◽

Loss Of Function ◽

Variant Discovery ◽

Pathogenic Variants ◽

Whole Exome ◽

Neurodevelopmental Problems

AbstractBackgroundA substantial portion of Mendelian disease patients suffers from genetic variants that are inherited in a recessive manner. A precise understanding of pathogenic recessive variants in a population would assist in pre-screening births of such patients. However, a systematic understanding of the contribution of recessive variants to Mendelian diseases is still lacking.MethodsGenetic diagnosis and variant discovery of 553 undiagnosed Korean patients with complex neurodevelopmental problems (KND for Korean NeuroDevelopmental cohort) were performed using whole exome sequencing of patients and their parents. Pathogenic variants were selected and evaluated based on a comparison to patient symptoms and genetic properties of the variants were analyzed.ResultsDisease-causing variants, including newly discovered variants, were identified in in 57.5% of the probands of the KND cohort. Of the 553 patients, 47.4% harbored variants that were previously reported as being pathogenic, and 35.1% of the previous reported pathogenic variants were inherited in a recessive manner. Genes that cause recessive disorders tend to be less constrained by loss-of-function variants and enriched in metabolic and mitochondrial pathways. This observation was applied to an estimation that approximately 1 in 17 healthy Korean individuals carry at least one of these pathogenic variants that develop severe neurodevelopmental problems in a recessive manner. Furthermore, the feasibility of these genes for carrier screening was evaluated.ConclusionsWe suggest that the odds are high for healthy individuals carrying a potentially pathogenic variant, and its genetic properties. Our results will serve as a foundation for recessive variant screening to reduce occurrences of rare Mendelian disease patients. Additionally, our results highlight the utility and necessity of whole exome sequencing-based diagnostics for improving patient care in a country with a centralized medical system.

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Analysis of the androgen receptor (AR) gene in a cohort of Indonesian undermasculinized 46, XY DSD patients

Egyptian Journal of Medical Human Genetics ◽

10.1186/s43042-021-00134-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Nurin Aisyiyah Listyasari ◽

Achmad Zulfa Juniarto ◽

Gorjana Robevska ◽

Katie L. Ayers ◽

Andrew H. Sinclair ◽

...

Keyword(s):

Androgen Receptor ◽

Sanger Sequencing ◽

Genetic Diagnosis ◽

Gonadal Development ◽

Androgen Insensitivity Syndrome ◽

Clinical Database ◽

Pathogenic Variants ◽

Indonesian Population ◽

Whole Exome ◽

Development And Differentiation

Abstract Background Pathogenic variants in the androgen receptor (AR) gene located on chromosome Xq11-12, are known to cause varying degrees of undermasculinization in 46, XY individuals. The aim of this study was to investigate the frequency of pathogenic variants in the AR gene in a cohort of 46, XY undermasculinized individuals from Indonesia who were suspected of having androgen insensitivity syndrome (AIS). All patients with 46, XY DSD referred to our center between 1994 and 2019 were collected from our clinical database. All 46, XY DSD patients without a prior molecular diagnosis with an external masculinization score (EMS) ≤ 9 were included in this study. All exons and intron–exon boundaries of AR gene were analyzed using Sanger sequencing to identify pathogenic variants of the AR gene. Results A cohort of 75 undermasculinized patients were selected for the study. Direct Sanger sequencing of all eight exons of the AR gene led to a genetic diagnosis in 11 patients (14.67%). All of the variants identified (p.Arg841His; p.Ile604Asn; p.Val731Met; p.Pro672Ser; p.Gln739Arg; p.Ser302Glufs*3) have been previously reported in patients with AIS. Conclusions This is the first study in Indonesia that highlights the significance of molecular analysis in providing a definitive diagnosis of AIS for patients with 46, XY DSD undermasculinization. This is an uncommon finding in the Indonesian population presenting with 46, XY DSD undermasculinization. A genetic diagnosis allows optimal clinical management and genetic counseling for patients and their families. As 46, XY DSD can be caused by pathogenic variants in other genes involved in gonadal development and differentiation, further genetic analysis, such as whole exome sequencing, should be carried out on those patients that did not carry an AR variant.

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Phenotypic spectrum and genomics of undiagnosed arthrogryposis multiplex congenita

Journal of Medical Genetics ◽

10.1136/jmedgenet-2020-107595 ◽

2021 ◽

pp. jmedgenet-2020-107595

Author(s):

Annie Laquerriere ◽

Dana Jaber ◽

Emanuela Abiusi ◽

Jérome Maluenda ◽

Dan Mejlachowicz ◽

...

Keyword(s):

Exome Sequencing ◽

De Novo ◽

Genetic Diagnosis ◽

Added Value ◽

Disease Genes ◽

Arthrogryposis Multiplex Congenita ◽

Pathogenic Variants ◽

New Genes ◽

Whole Exome ◽

Disease Loci

BackgroundArthrogryposis multiplex congenita (AMC) is characterised by congenital joint contractures in two or more body areas. AMC exhibits wide phenotypic and genetic heterogeneity. Our goals were to improve the genetic diagnosis rates of AMC, to evaluate the added value of whole exome sequencing (WES) compared with targeted exome sequencing (TES) and to identify new genes in 315 unrelated undiagnosed AMC families.MethodsSeveral genomic approaches were used including genetic mapping of disease loci in multiplex or consanguineous families, TES then WES. Sanger sequencing was performed to identify or validate variants.ResultsWe achieved disease gene identification in 52.7% of AMC index patients including nine recently identified genes (CNTNAP1, MAGEL2, ADGRG6, ADCY6, GLDN, LGI4, LMOD3, UNC50 and SCN1A). Moreover, we identified pathogenic variants in ASXL3 and STAC3 expanding the phenotypes associated with these genes. The most frequent cause of AMC was a primary involvement of skeletal muscle (40%) followed by brain (22%). The most frequent mode of inheritance is autosomal recessive (66.3% of patients). In sporadic patients born to non-consanguineous parents (n=60), de novo dominant autosomal or X linked variants were observed in 30 of them (50%).ConclusionNew genes recently identified in AMC represent 21% of causing genes in our cohort. A high proportion of de novo variants were observed indicating that this mechanism plays a prominent part in this developmental disease. Our data showed the added value of WES when compared with TES due to the larger clinical spectrum of some disease genes than initially described and the identification of novel genes.

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