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Artykuły w czasopismach na temat „Causative variants”

Autor: Grafiati
Data publikacji: 12 października 2024
Data aktualizacji: 31 lipca 2025

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1

Pareja, Fresia, Ryan N. Ptashkin, David N. Brown, et al. "Cancer-Causative Mutations Occurring in Early Embryogenesis." Cancer Discovery 12, no. 4 (2021): 949–57. http://dx.doi.org/10.1158/2159-8290.cd-21-1110.

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Abstract Mosaic mutations in normal tissues can occur early in embryogenesis and be associated with hereditary cancer syndromes when affecting cancer susceptibility genes (CSG). Their contribution to apparently sporadic cancers is currently unknown. Analysis of paired tumor/blood sequencing data of 35,310 patients with cancer revealed 36 pathogenic mosaic variants affecting CSGs, most of which were not detected by prior clinical genetic testing. These CSG mosaic variants were consistently detected at varying variant allelic fractions in microdissected normal tissues (n = 48) from distinct embr
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2

Shakil, Muhammad, Abida Akbar, Nazish Mahmood Aisha, et al. "Delineating Novel and Known Pathogenic Variants in TYR, OCA2 and HPS-1 Genes in Eight Oculocutaneous Albinism (OCA) Pakistani Families." Genes 13, no. 3 (2022): 503. http://dx.doi.org/10.3390/genes13030503.

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Oculocutaneous albinism (OCA) is associated with a wide range of clinical presentations and has been categorized with syndromic and non-syndromic features. The most common causative genes in non-syndromic OCA are TYR and OCA2 and HSP1 is in the syndromic albinism. The objective of this study was to identify pathogenic variants in congenital OCA families from Pakistan. Eight consanguineous families were recruited, and clinical and ophthalmological examination was carried out to diagnose the disease. Whole blood was collected from the participating individuals, and genomic DNA was extracted for
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3

Thanikachalam, Saradadevi, Elizabeth Hodapp, Ta C. Chang, et al. "Spectrum of Genetic Variants Associated with Anterior Segment Dysgenesis in South Florida." Genes 11, no. 4 (2020): 350. http://dx.doi.org/10.3390/genes11040350.

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Anterior segment dysgenesis (ASD) comprises a wide spectrum of developmental conditions affecting the cornea, iris, and lens, which may be associated with abnormalities of other organs. To identify disease-causing variants, we performed exome sequencing in 24 South Florida families with ASD. We identified 12 likely causative variants in 10 families (42%), including single nucleotide or small insertion–deletion variants in B3GLCT, BMP4, CYP1B1, FOXC1, FOXE3, GJA1, PXDN, and TP63, and a large copy number variant involving PAX6. Four variants were novel. Each variant was detected only in one fami
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4

Bengani, Hemant, Detelina Grozeva, Lambert Moyon, et al. "Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability." PLOS ONE 16, no. 8 (2021): e0256181. http://dx.doi.org/10.1371/journal.pone.0256181.

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Identifying causative variants in cis-regulatory elements (CRE) in neurodevelopmental disorders has proven challenging. We have used in vivo functional analyses to categorize rigorously filtered CRE variants in a clinical cohort that is plausibly enriched for causative CRE mutations: 48 unrelated males with a family history consistent with X-linked intellectual disability (XLID) in whom no detectable cause could be identified in the coding regions of the X chromosome (chrX). Targeted sequencing of all chrX CRE identified six rare variants in five affected individuals that altered conserved bas
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5

Wuyun, Saina. "Causative alternation in Zuo Tradition." Language and Linguistics / 語言暨語言學 25, no. 1 (2024): 123–61. http://dx.doi.org/10.1075/lali.00151.wuy.

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Abstract This study examines the different variants of causative alternation in Zuo Tradition (左傳), an archaic Chinese narrative history from the Pre-Qin period. It is found that denominal verbs, unergative verbs, and “pure” unaccusative verbs participate actively in the alternation, and that the causative variant bears a complex relation with the agentive and putative variants; this causes problems for previous analyses. This paper proposes a two-step build-up of eventuality for causative alternation in archaic Chinese. Specifically, I propose that verbs in archaic Chinese are monadic and sel
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6

Di Taranto, Maria Donata, and Giuliana Fortunato. "Genetic Heterogeneity of Familial Hypercholesterolemia: Repercussions for Molecular Diagnosis." International Journal of Molecular Sciences 24, no. 4 (2023): 3224. http://dx.doi.org/10.3390/ijms24043224.

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Genetics of Familial Hypercholesterolemia (FH) is ascribable to pathogenic variants in genes encoding proteins leading to an impaired LDL uptake by the LDL receptor (LDLR). Two forms of the disease are possible, heterozygous (HeFH) and homozygous (HoFH), caused by one or two pathogenic variants, respectively, in the three main genes that are responsible for the autosomal dominant disease: LDLR, APOB and PCSK9 genes. The HeFH is the most common genetic disease in humans, being the prevalence about 1:300. Variants in the LDLRAP1 gene causes FH with a recessive inheritance and a specific APOE var
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7

Thongnak, Chuphong, Areerat Hnoonual, Duangkamol Tangviriyapaiboon, et al. "Whole-Exome Sequencing Identifies One De Novo Variant in the FGD6 Gene in a Thai Family with Autism Spectrum Disorder." International Journal of Genomics 2018 (2018): 1–7. http://dx.doi.org/10.1155/2018/8231547.

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Autism spectrum disorder (ASD) has a strong genetic basis, although the genetics of autism is complex and it is unclear. Genetic testing such as microarray or sequencing was widely used to identify autism markers, but they are unsuccessful in several cases. The objective of this study is to identify causative variants of autism in two Thai families by using whole-exome sequencing technique. Whole-exome sequencing was performed with autism-affected children from two unrelated families. Each sample was sequenced on SOLiD 5500xl Genetic Analyzer system followed by combined bioinformatics pipeline
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8

Moyon, Lambert, Camille Berthelot, Alexandra Louis, Nga Thi Thuy Nguyen, and Hugues Roest Crollius. "Classification of non-coding variants with high pathogenic impact." PLOS Genetics 18, no. 4 (2022): e1010191. http://dx.doi.org/10.1371/journal.pgen.1010191.

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Whole genome sequencing is increasingly used to diagnose medical conditions of genetic origin. While both coding and non-coding DNA variants contribute to a wide range of diseases, most patients who receive a WGS-based diagnosis today harbour a protein-coding mutation. Functional interpretation and prioritization of non-coding variants represents a persistent challenge, and disease-causing non-coding variants remain largely unidentified. Depending on the disease, WGS fails to identify a candidate variant in 20–80% of patients, severely limiting the usefulness of sequencing for personalised med
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9

Ridgeway, Anna R., Ciara Shortall, Laura K. Finnegan, et al. "Novel Splice-Altering Variants in the CHM and CACNA1F Genes Causative of X-Linked Choroideremia and Cone Dystrophy." Genes 16, no. 1 (2024): 25. https://doi.org/10.3390/genes16010025.

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Background: An estimated 10–15% of all genetic diseases are attributable to variants in noncanonical splice sites, auxiliary splice sites and deep-intronic variants. Most of these unstudied variants are classified as variants of uncertain significance (VUS), which are not clinically actionable. This study investigated two novel splice-altering variants, CHM NM_000390.4:c.941-11T>G and CACNA1F NM_005183.4:c.2576+4_2576+5del implicated in choroideremia and cone dystrophy (COD), respectively, resulting in significant visual loss. Methods: Next-generation sequencing was employed to identify the
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10

Monasky, Michelle M., Emanuele Micaglio, Giuseppe Ciconte, and Carlo Pappone. "Brugada Syndrome: Oligogenic or Mendelian Disease?" International Journal of Molecular Sciences 21, no. 5 (2020): 1687. http://dx.doi.org/10.3390/ijms21051687.

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Brugada syndrome (BrS) is diagnosed by a coved-type ST-segment elevation in the right precordial leads on the electrocardiogram (ECG), and it is associated with an increased risk of sudden cardiac death (SCD) compared to the general population. Although BrS is considered a genetic disease, its molecular mechanism remains elusive in about 70–85% of clinically-confirmed cases. Variants occurring in at least 26 different genes have been previously considered causative, although the causative effect of all but the SCN5A gene has been recently challenged, due to the lack of systematic, evidence-bas
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11

Thomas, Laurent F., Takaya Saito, and Pål Sætrom. "Inferring causative variants in microRNA target sites." Nucleic Acids Research 39, no. 16 (2011): e109-e109. http://dx.doi.org/10.1093/nar/gkr414.

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12

Boudellioua, Imane, Rozaimi B. Mahamad Razali, Maxat Kulmanov, et al. "Semantic prioritization of novel causative genomic variants." PLOS Computational Biology 13, no. 4 (2017): e1005500. http://dx.doi.org/10.1371/journal.pcbi.1005500.

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13

Abdelkader, Ehab, Oliver Brandau, Carsten Bergmann, Nuha AlSalamah, Sawsan Nowilaty, and Patrik Schatz. "Novel causative variants in patients with achromatopsia." Ophthalmic Genetics 39, no. 6 (2018): 678–83. http://dx.doi.org/10.1080/13816810.2018.1522653.

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14

Shchagina, Olga, Mariya Orlova, Aisylu Murtazina, Alexandra Filatova, Mikhail Skoblov, and Elena Dadali. "Evaluation of Pathogenicity and Causativity of Variants in the MPZ and SH3TC2 Genes in a Family Case of Hereditary Peripheral Neuropathy." International Journal of Molecular Sciences 24, no. 12 (2023): 9786. http://dx.doi.org/10.3390/ijms24129786.

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The implementation of NGS methods into clinical practice allowed researchers effectively to establish the molecular cause of a disorder in cases of a genetically heterogeneous pathology. In cases of several potentially causative variants, we need additional analysis that can help in choosing a proper causative variant. In the current study, we described a family case of hereditary motor and sensory neuropathy (HMSN) type 1 (Charcot–Marie–Tooth disease). DNA analysis revealed two variants in the SH3TC2 gene (c.279G>A and c.1177+5G>A), as well as a previously described variant c.449−9C>
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15

Myasnikov, Roman P., Olga V. Kulikova, Alexey N. Meshkov, et al. "A Splice Variant of the MYH7 Gene Is Causative in a Family with Isolated Left Ventricular Noncompaction Cardiomyopathy." Genes 13, no. 10 (2022): 1750. http://dx.doi.org/10.3390/genes13101750.

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Variants of the MYH7 gene have been associated with a number of primary cardiac conditions, including left ventricular noncompaction cardiomyopathy (LVNC). Most cases of MYH7-related diseases are associated with such variant types as missense substitutions and in-frame indels. Thus, truncating variants in MYH7 (MYH7tv) and associated mechanism of haploinsufficiency are usually considered not pathogenic in these disorders. However, recent large-scale studies demonstrated evidence of the significance of MYH7tv for LVNC and gave rise to an assumption that haploinsufficiency may be the causal mech
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16

Lourenco, Daniela, Shogo Tsuruta, Sungbong Jang, Breno O. Fragomeni, and Ignacy Misztal. "41 Using Sequence Data to Increase Accuracy of Genomic Predictions in Livestock: Are We There Yet?" Journal of Animal Science 99, Supplement_3 (2021): 22–23. http://dx.doi.org/10.1093/jas/skab235.037.

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Abstract As sequence data is becoming available for many livestock species, there is a question on whether this information can help to boost the accuracy of genomic predictions beyond what has already been achieved with SNP chips. Several studies have been conducted by our group using simulated and real livestock populations that included from 1,000 to 100,000 animals with full or imputed sequence information. For the real datasets, the potential causative variants were identified based on genome-wide association (GWA) and were added to the current SNP chips. Additional scenarios included the
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17

Biswas, Pooja, Adda L. Villanueva, Angel Soto-Hermida, et al. "Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis." PLOS Genetics 17, no. 10 (2021): e1009848. http://dx.doi.org/10.1371/journal.pgen.1009848.

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Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including
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18

Letko, Anna, Fabienne Leuthard, Vidhya Jagannathan, et al. "Whole Genome Sequencing Indicates Heterogeneity of Hyperostotic Disorders in Dogs." Genes 11, no. 2 (2020): 163. http://dx.doi.org/10.3390/genes11020163.

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Craniomandibular osteopathy (CMO) and calvarial hyperostotic syndrome (CHS) are proliferative, non-neoplastic disorders affecting the skull bones in young dogs. Different forms of these hyperostotic disorders have been described in many dog breeds. However, an incompletely dominant causative variant for CMO affecting splicing of SLC37A2 has been reported so far only in three Terrier breeds. The purpose of this study was to identify further possible causative genetic variants associated with CHS in an American Staffordshire Terrier, as well as CMO in seven affected dogs of different breeds. We
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19

Matczyńska, Ewa, Robert Szymańczak, Katarzyna Stradomska, et al. "Whole-Exome Analysis for Polish Caucasian Patients with Retinal Dystrophies and the Creation of a Reference Genomic Database for the Polish Population." Genes 15, no. 8 (2024): 1011. http://dx.doi.org/10.3390/genes15081011.

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We present the results of the first study of a large cohort of patients with inherited retinal dystrophies (IRD) performed for the Polish population using whole-exome sequencing (WES) in the years 2016–2019. Moreover, to facilitate such diagnostic analyses and enable future application of gene therapy and genome editing for IRD patients, a Polish genomic reference database (POLGENOM) was created based on whole-genome sequences of healthy Polish Caucasian nonagenarians and centenarians. The newly constructed database served as a control, providing a comparison for variant frequencies in the Pol
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20

Majeres, Leif E., Anna C. Dilger, Daniel W. Shike, Joshua C. McCann, and Jonathan E. Beever. "Defining a Haplotype Encompassing the LCORL-NCAPG Locus Associated with Increased Lean Growth in Beef Cattle." Genes 15, no. 5 (2024): 576. http://dx.doi.org/10.3390/genes15050576.

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Numerous studies have shown genetic variation at the LCORL-NCAPG locus is strongly associated with growth traits in beef cattle. However, a causative molecular variant has yet to be identified. To define all possible candidate variants, 34 Charolais-sired calves were whole-genome sequenced, including 17 homozygous for a long-range haplotype associated with increased growth (QQ) and 17 homozygous for potential ancestral haplotypes for this region (qq). The Q haplotype was refined to an 814 kb region between chr6:37,199,897–38,014,080 and contained 218 variants not found in qq individuals. These
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21

Niitsuma, Sou, Hiroki Kudo, Atsuo Kikuchi, et al. "Biallelic variants/mutations of IL1RAP in patients with steroid-sensitive nephrotic syndrome." International Immunology 32, no. 4 (2019): 283–92. http://dx.doi.org/10.1093/intimm/dxz081.

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Abstract Nephrotic syndrome (NS) is a renal disease characterized by severe proteinuria and hypoproteinemia. Although several single-gene mutations have been associated with steroid-resistant NS, causative genes for steroid-sensitive NS (SSNS) have not been clarified. While seeking to identify causative genes associated with SSNS by whole-exome sequencing, we found compound heterozygous variants/mutations (c.524T>C; p.I175T and c.662G>A; p.R221H) of the interleukin-1 receptor accessory protein (IL1RAP) gene in two siblings with SSNS. The siblings’ parents are healthy, and each pa
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Bernal Barquero, Carlos Eduardo, Romina Celeste Geysels, Virginie Jacques, et al. "Targeted Next-Generation Sequencing of Congenital Hypothyroidism-Causative Genes Reveals Unexpected Thyroglobulin Gene Variants in Patients with Iodide Transport Defect." International Journal of Molecular Sciences 23, no. 16 (2022): 9251. http://dx.doi.org/10.3390/ijms23169251.

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Congenital iodide transport defect is an uncommon autosomal recessive disorder caused by loss-of-function variants in the sodium iodide symporter (NIS)-coding SLC5A5 gene and leading to dyshormonogenic congenital hypothyroidism. Here, we conducted a targeted next-generation sequencing assessment of congenital hypothyroidism-causative genes in a cohort of nine unrelated pediatric patients suspected of having a congenital iodide transport defect based on the absence of 99mTc-pertechnetate accumulation in a eutopic thyroid gland. Although, unexpectedly, we could not detect pathogenic SLC5A5 gene
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23

Akouchekian, Mansoureh, Mitra Hakim Shooshtari, Hamed Heidary, Fateme Zahedi Abghari, and Parisa Moeinian. "The causative variants of amyloidosis in the autism." International Journal of Neuroscience 129, no. 1 (2018): 10–15. http://dx.doi.org/10.1080/00207454.2018.1503177.

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Chan, Jacqueline, Jolyon Holdstock, John Shovelton, et al. "Clinical and analytical validation of an 82-gene comprehensive genome-profiling panel for identifying and interpreting variants responsible for inherited retinal dystrophies." PLOS ONE 19, no. 6 (2024): e0305422. http://dx.doi.org/10.1371/journal.pone.0305422.

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Inherited retinal dystrophies comprise a clinically complex and heterogenous group of diseases characterized by visual impairment due to pathogenic variants of over 300 different genes. Accurately identifying the causative gene and associated variant is crucial for the definitive diagnosis and subsequent selection of precise treatments. Consequently, well-validated genetic tests are required in the clinical practice. Here, we report the analytical and clinical validation of a next-generation sequencing targeted gene panel, the PrismGuide IRD Panel System. This system enables comprehensive geno
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Abu-Rub, Lubna I., Tara Al-Barazenji, Sumaya Abiib, et al. "Identification of KSR2 Variants in Pediatric Patients with Severe Early-Onset Obesity from Qatar." Genes 15, no. 8 (2024): 966. http://dx.doi.org/10.3390/genes15080966.

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The kinase suppressor of Ras 2 (KSR2) gene is associated with monogenic obesity, and loss-of-function variants in KSR2 have been identified in individuals with severe early-onset obesity. This study investigated KSR2 variants in 9 pediatric patients with severe early-onset obesity in Qatar using whole genome sequencing among a cohort of 240 individuals. We focused on KSR2 variants with a minor allele frequency (MAF) below 1% and a Combined Annotation Dependent Depletion (CADD) score above 13 to identify potential causative variants. Our analysis identified four KSR2 variants: one intronic (c.1
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26

Siutkina, Nadezhda P., and Svetlana V. Shustova. "COGNITIVE SCENARIO OF CAUSATIVE VERB "REIZEN" IN THE GERMAN LANGUAGE: ON THE ISSUE OF SEMANTIC POTENTIAL EXPANSION." Theoretical and Applied Linguistics, no. 1 (2018): 84–91. http://dx.doi.org/10.22250/2410-7190_2018_4_1_84_91.

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The article focuses upon the features of the semantic potential of the emotive causative reizen. Emotive causatives are understood as causative verbs denoting interpersonal interaction resulting in modification of the emotional and psychological state of the subject. There are causatives actualizing positive and negative tone as well as axiological neutral state. The peculiarity of the verb reizen is that it can actualize all the three variants of emotional modification. The research is carried out in the aspect of functional grammar on the example of the semantic categories of causativeness,
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27

Takao, Akinari, Tatsuro Yamaguchi, Hidetaka Eguchi, et al. "Genetic testing of Japanese patients with serrated polyposis syndrome: A multicentric study." Journal of Clinical Oncology 42, no. 3_suppl (2024): 75. http://dx.doi.org/10.1200/jco.2024.42.3_suppl.75.

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75 Background: Serrated polyposis syndrome (SPS) is a rare condition associated with an increased risk of colorectal cancer. Previous studies have identified germline truncating variants of the RNF43; however, patients harboring these variants comprise a small part of those with SPS, in most of whom the causative gene remains unknown. To date, no study has described the genetic features of Japanese patients with SPS. The present study aimed to identify candidate causative genes of SPS in Japanese patients. Methods: Captures for equal to or more than 55 gene regions were performed using Agilent
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28

Rasia, Maria Eugenia Mangialavori. "Stativity in the Causative Alternation? New Questions and a New Variant." Open Linguistics 5, no. 1 (2019): 233–59. http://dx.doi.org/10.1515/opli-2019-0014.

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AbstractThis paper discusses whether capacity to license an internal argument and eventivity are default properties of so-called change-of-state verbs.I draw attention to the claim that, in certain languages, the causative-inchoative alternation extends to a third, external-argument-only variant with stative behavior. Productivity and systematicity raise a host of problems for current generalizations on the Causative Alternation and change-of-state verbs for various reasons, starting from the long-held claim that unique arguments of change-of-state verbs are by default internal. Insofar as the
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29

Naruse, Hiroya, Hiroyuki Ishiura, Jun Mitsui, et al. "Burden of rare variants in causative genes for amyotrophic lateral sclerosis (ALS) accelerates age at onset of ALS." Journal of Neurology, Neurosurgery & Psychiatry 90, no. 5 (2018): 537–42. http://dx.doi.org/10.1136/jnnp-2018-318568.

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ObjectivesTo evaluate the burden of rare variants in the causative genes for amyotrophic lateral sclerosis (ALS) on the age at onset of ALS in a Japanese case series.MethodsWe conducted whole-exome sequencing analysis of 89 families with familial ALS (FALS) and 410 patients with sporadic ALS (SALS) to identify known pathogenic mutations or rare functionally predicted deleterious variants in the causative genes for ALS. Rare variants (minor allele frequency <1%) with scaled Combined Annotation-Dependent Depletion score >20 were defined as rare functionally predicted deleterious variants.
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30

Savelyev, V. N., I. V. Savelyeva, B. V. Babenyshev, and A. N. Kulichenko. "The evolution of the pathogen and the clinical and epidemiological features of the recent cholera (el tor)." Epidemiology and Infectious Diseases 17, no. 5 (2012): 31–35. http://dx.doi.org/10.17816/eid40707.

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In a comparative perspective studied cholera outbreak in the Caucasus due to typical toxigenic and genetically modified (hybrid) El Tor variant strains have been studied. Revealed features of the genetic structure of the genome, factors and ways of transmission of the causative agent of modern cholera El tor should be considered when improving the program of epidemiological supervision in terms of enhancing antiepidemic and prevention measures in cholera, the causative factor of which are of hybrid variants of Vibrio cholerae El tor.
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Zhang, Lujia, Ya Li, Litao Qin, Yu Wu, and Bo Lei. "Autosomal Recessive Retinitis Pigmentosa Associated with Three Novel REEP6 Variants in Chinese Population." Genes 12, no. 4 (2021): 537. http://dx.doi.org/10.3390/genes12040537.

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Retinitis pigmentosa 77 is caused by mutations of REEP6 (MIM: 609346), which encodes a protein for the development of photoreceptors. Our study was to identify disease-causing variants in three Chinese families using targeted next-generation sequencing (NGS). Multiple lines of computational predictions combined with in vitro cellular experiments were applied to evaluate the pathogenicity of the newly found variants. Three novel variants in REEP6, including one missense variant, c.268G>C, one frameshift variant, c.468delC, and one splicing variant, c.598+1G>C, were found, while c.268G>
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Alesi, Viola, Maria Lisa Dentici, Silvia Genovese, et al. "Homozygous HESX1 and COL1A1 Gene Variants in a Boy with Growth Hormone Deficiency and Early Onset Osteoporosis." International Journal of Molecular Sciences 22, no. 2 (2021): 750. http://dx.doi.org/10.3390/ijms22020750.

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We report on a patient born to consanguineous parents, presenting with Growth Hormone Deficiency (GHD) and osteoporosis. SNP-array analysis and exome sequencing disclosed long contiguous stretches of homozygosity and two distinct homozygous variants in HESX1 (Q6H) and COL1A1 (E1361K) genes. The HESX1 variant was described as causative in a few subjects with an incompletely penetrant dominant form of combined pituitary hormone deficiency (CPHD). The COL1A1 variant is rare, and so far it has never been found in a homozygous form. Segregation analysis showed that both variants were inherited from
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Suzuki, Yasuo, Kan Katayama, Ryosuke Saiki, et al. "Mutation Analysis of Autosomal-Dominant Polycystic Kidney Disease Patients." Genes 14, no. 2 (2023): 443. http://dx.doi.org/10.3390/genes14020443.

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Autosomal-dominant polycystic kidney disease (ADPKD) is characterized by bilateral kidney cysts that ultimately lead to end-stage kidney disease. While the major causative genes of ADPKD are PKD1 and PKD2, other genes are also thought to be involved. Fifty ADPKD patients were analyzed by exome sequencing or multiplex ligation-dependent probe amplification (MLPA), followed by long polymerase chain reaction and Sanger sequencing. Variants in PKD1 or PKD2 or GANAB were detected in 35 patients (70%). Exome sequencing identified 24, 7, and 1 variants in PKD1, PKD2, and GANAB, respectively, in 30 pa
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KOCAAĞA, Ayça, and Hatice Mine ÇAKMAK. "Identification of Novel Mutations in Children with Hereditary Spherocytosis by Targeted Exome Sequencing: A Single Center Experience." Medical Journal of Western Black Sea 6, no. 3 (2022): 296–301. http://dx.doi.org/10.29058/mjwbs.1200958.

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Aim: Hereditary spherocytosis (HS) is a prevalent cause of congenital hemolytic anemia in Northern
 Europeans. It is characterized by spherocytes resulting from defects in the erythrocyte structural
 membrane proteins spectrin and ankyrin. To date, more than five candidate genes, including ANK1,
 SPTB, SPTA1, SLC4A1, and EPB42 have been linked to HS. Here, we aim to investigate the presence
 of novel as well as known mutations in eight Turkish children with clinically suspected HS.
 Material and Methods: We presented the clinical features of the patients and identified
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Schlingmann, Karl P., François Jouret, Kuang Shen, et al. "mTOR-Activating Mutations in RRAGD Are Causative for Kidney Tubulopathy and Cardiomyopathy." Journal of the American Society of Nephrology 32, no. 11 (2021): 2885–99. http://dx.doi.org/10.1681/asn.2021030333.

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BackgroundOver the last decade, advances in genetic techniques have resulted in the identification of rare hereditary disorders of renal magnesium and salt handling. Nevertheless, approximately 20% of all patients with tubulopathy lack a genetic diagnosis.MethodsWe performed whole-exome and -genome sequencing of a patient cohort with a novel, inherited, salt-losing tubulopathy; hypomagnesemia; and dilated cardiomyopathy. We also conducted subsequent in vitro functional analyses of identified variants of RRAGD, a gene that encodes a small Rag guanosine triphosphatase (GTPase).ResultsIn eight ch
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Guo, Jing, Owen J. L. Rackham, Niina Sandholm, et al. "Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy." Journal of the American Society of Nephrology 31, no. 2 (2020): 309–23. http://dx.doi.org/10.1681/asn.2019030289.

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BackgroundSeveral genetic susceptibility loci associated with diabetic nephropathy have been documented, but no causative variants implying novel pathogenetic mechanisms have been elucidated.MethodsWe carried out whole-genome sequencing of a discovery cohort of Finnish siblings with type 1 diabetes who were discordant for the presence (case) or absence (control) of diabetic nephropathy. Controls had diabetes without complications for 15–37 years. We analyzed and annotated variants at genome, gene, and single-nucleotide variant levels. We then replicated the associated variants, genes, and regi
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Dianat, Tahereh, Dor Mohammad Kordi Tamandani, Maryam Najafi, and Ali Khajeh. "Novel WDR62 and MTR Variants in a Patient With Autosomal Recessive Primary Microcephaly-2 With Polymicrogyria and Homocystinuria-Megaloblastic Anemia." Disease and Diagnosis 11, no. 4 (2022): 142–46. http://dx.doi.org/10.34172/ddj.2022.27.

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Background: Autosomal recessive primary microcephaly-2 (MCPH2) is a rare genetic disorder with clinical and genetic heterogeneity. This study aimed to perform high-throughput whole-exome sequencing (WES) to facilitate the diagnosis of the genetic variants responsible for MCPH2 and the comorbidities. Materials and Methods: The WES was performed for a 3-year-old boy with primary microcephaly-2 and homocystinuria-megaloblastic anemia in a consanguineous family. Sequencing and variant calling was conducted by standard bioinformatics tools. Filtering was performed to prioritize novel variants. Fina
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Fragomeni, B. D., D. A. L. Lourenco, Y. Masuda, A. Legarra, and I. Misztal. "193 Including causative variants into single step genomic BLUP." Journal of Animal Science 95, suppl_4 (2017): 95–96. http://dx.doi.org/10.2527/asasann.2017.193.

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Johnsson, Martin, and Melissa K. Jungnickel. "Evidence for and localization of proposed causative variants in cattle and pig genomes." Genetics Selection Evolution 53, no. 1 (2021). http://dx.doi.org/10.1186/s12711-021-00662-x.

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Abstract Background This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. Results For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PH
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Inoue, Michio, Yoshihiko Saito, Takahiro Yonekawa, et al. "Causative variant profile of collagen VI-related dystrophy in Japan." Orphanet Journal of Rare Diseases 16, no. 1 (2021). http://dx.doi.org/10.1186/s13023-021-01921-2.

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Abstract Background Collagen VI-related dystrophy spans a clinical continuum from severe Ullrich congenital muscular dystrophy to milder Bethlem myopathy. This disease is caused by causative variants in COL6A1, COL6A2, or COL6A3. Most reported causative variants are de novo; therefore, to identify possible associated causative variants, comprehensive large cohort studies are required for different ethnicities. Methods We retrospectively reviewed clinical information, muscle histology, and genetic analyses from 147 Japanese patients representing 130 families, whose samples were sent for diagnos
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Brabbing‐Goldstein, Dana, Lily Bazak, Noa Ruhrman‐Shahar, et al. "Potentially Missed Diagnoses in Prenatal Versus Postnatal Exome Sequencing in the Lack of Informative Phenotype: Lessons Learned From a Postnatal Cohort." Prenatal Diagnosis, September 5, 2024. http://dx.doi.org/10.1002/pd.6659.

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ABSTRACTObjectiveTo investigate how many novel pathogenic (P) and likely pathogenic (LP) nonprotein‐truncating or noncanonical splicing variants would be classified as variants of unknown significance (VUS) if they were detected in fetuses without abnormalities.MethodsThe study included 156 patients with neurodevelopmental disorders diagnosed through postnatal exome sequencing. Causative P/LP nonprotein‐truncating and noncanonical splicing variants were retrospectively reclassified in cases without specific prenatal manifestations, disregarding postnatal symptoms.ResultsOf the 156 patients, 72
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Seo, Yuri, Tae Young Kim, Dongju Won, et al. "Genetic spectrum and characteristics of autosomal optic neuropathy in Korean: Use of next-generation sequencing in suspected hereditary optic atrophy." Frontiers in Neurology 13 (August 22, 2022). http://dx.doi.org/10.3389/fneur.2022.978532.

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AimsTo evaluate the clinical characteristics and causative genetic variants in autosomal optic atrophy diagnosed using next-generation sequencing (NGS).MethodsA cohort of 57 unrelated families affected with bilateral optic atrophy were recruited from two university-based tertiary referral hospitals from May 2016 to April 2022. Genetic variants were detected using a target enrichment panel consisting of 429 or 595 genes and known deep intronic variants associated with inherited eye diseases, exome sequencing, or genome sequencing. The results of detailed clinical examinations, disease-causing v
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Stutterd, Chloe A., Stefanie Brock, Katrien Stouffs, et al. "Genetic heterogeneity of polymicrogyria: study of 123 patients using deep sequencing." Brain Communications, December 26, 2020. http://dx.doi.org/10.1093/braincomms/fcaa221.

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Abstract Polymicrogyria is a malformation of cortical development characterized by overfolding and abnormal lamination of the cerebral cortex. Manifestations include epilepsy, speech disturbance and motor and cognitive disability. Causes include acquired prenatal insults and inherited and de novo genetic variants. The proportion of patients with polymicrogyria and a causative germline or mosaic variant is not known. The aim of this study was to identify the monogenic causes of polymicrogyria in a heterogeneous cohort of patients reflective of specialized referral services. Patients with polymi
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Dahlin, Maria, Tommy Stödberg, Elin Ekman, Virpi Töhönen, and Anna Wedell. "Genetic aetiologies in relation to response to the ketogenic diet in 226 children with epilepsy." Brain Communications, April 5, 2025. https://doi.org/10.1093/braincomms/fcaf134.

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Abstract A ketogenic diet is used in children with drug-resistant epilepsy but predictors for efficacy are largely lacking. Our aim was to evaluate if causative genetic variants could predict seizure response to the ketogenic diet. A cohort study of 226 children with refractory epilepsy and classic ketogenic diet treatment for at least 3 months (76.9% of the 294 who started) was performed. The median age at diet start was 5.1 years (range 0.1-17.8), 118 were girls and 108 boys. They had previous trials of a median of 6.0 antiseizure medications (range 0-12) and intellectual disability was foun
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Hori, Mika, Atsushi Takahashi, Kiminori Hosoda, Masatsune Ogura, and Mariko Harada-Shiba. "A low-frequency APOB p.(Pro955Ser) variant contributes to the severity of/variability in familial hypercholesterolemia." Journal of Clinical Endocrinology & Metabolism, October 3, 2022. http://dx.doi.org/10.1210/clinem/dgac572.

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ABSTRACT Context Heterozygous familial hypercholesterolemia (HeFH) is caused by a rare pathogenic variant in the LDLR, APOB and PCSK9 genes. However, the causative variants in these genes have not been identified in approximately 40% of HeFH patients.Objective: Our aim was to identify novel (or additional) genes/variants that contribute to HeFH. Methods Whole-exome sequencing was performed for 215 family members from 122 families with HeFH without pathogenic variants in the LDLR or PCSK9 genes. Results We could not find novel causative FH genes/variants by family analysis. Next, we examined al
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Ansari, Morad, Mihail Halachev, David Parry, et al. "Whole Genome Sequencing of “Mutation‐Negative” Individuals With Cornelia de Lange Syndrome." Human Mutation 2025, no. 1 (2025). https://doi.org/10.1155/humu/4711663.

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This study was aimed at assessing the diagnostic utility of whole genome sequence analysis in a well‐characterised research cohort of individuals referred with a clinical suspicion of Cornelia de Lange syndrome (CdLS) in whom prior genetic testing had not identified a causative variant. Short‐read whole genome sequencing was performed on 195 individuals from 105 families, 108 of whom were affected. 100/108 of the affected individuals had prior relevant genetic testing, with no pathogenic variant being identified. The study group comprised 42 trios in which both parental samples were available
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Eghbali, Maryam, Kiyana Sadat Fatemi, Shadab Salehpour, et al. "Whole-Exome Sequencing Uncovers Novel Causative Variants and Additional Findings in Three Patients Affected by Glycogen Storage Disease Type VI and Fanconi−Bickel Syndrome." Frontiers in Genetics 11 (January 11, 2021). http://dx.doi.org/10.3389/fgene.2020.601566.

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Glycogen storage diseases (GSDs) are the heterogeneous group of disorders caused by mutations in at least 30 different genes. Different types of GSDs, especially liver GSDs, take overlapping symptoms and can be clinically indistinguishable. This survey evaluated the use of whole-exome sequencing (WES) for the genetic analysis of the liver GSD-suspected patients in three unrelated families. An in-house filtering pipeline was used to assess rare pathogenic variants in GSD-associated genes, autosomal recessive/mendelian disorder genes (carrier status for genetic counseling subjects), and the ACMG
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Toyoda, Yu, Yusuke Kawamura, Akiyoshi Nakayama, et al. "Substantial anti-gout effect conferred by common and rare dysfunctional variants of URAT1/SLC22A12." Rheumatology, April 2, 2021. http://dx.doi.org/10.1093/rheumatology/keab327.

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Abstract Objectives Gout, caused by chronic elevation of serum uric acid levels, is the commonest form of inflammatory arthritis. The causative effect of common and rare variants of ATP-binding cassette transporter G2 (ABCG2/BCRP) on gout risk has been studied, but little attention has been paid to the effect of common (rs121907892, p.W258X) and rare variants of urate transporter 1 (URAT1/SLC22A12) on gout, despite dysfunctional variants of URAT1 having been identified as pathophysiological causes of renal hypouricaemia. Methods To address this important but overlooked issue, we investigated t
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Shinya, Y., T. Hiraide, M. Kataoka, et al. "A novel causative gene variant, TNFRSF13B p.Gly76Ser, in patients with pulmonary arterial hypertension." European Heart Journal 41, Supplement_2 (2020). http://dx.doi.org/10.1093/ehjci/ehaa946.2310.

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Abstract Background Pulmonary artery hypertension (PAH) is a poor prognostic disease. Some causative genes were reported as the PAH-associated genes. However, the pathogenetic variants in PAH-associated genes have not been identified in majority of patients with idiopathic PAH. Purpose Our aim was to investigate the new causative gene variants associated with PAH. Methods We performed whole-exome sequencing in 272 patients with idiopathic/heritable PAH. Structural analysis simulation was performed to define how the candidate gene variant affected the structure of protein. Results We identified
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Novelli, V., D. Mazza, M. Cammarano, et al. "P485Re-interpretation of variants of uncertain significance in inherited cardiovascular diseases-A pilot study." EP Europace 22, Supplement_1 (2020). http://dx.doi.org/10.1093/europace/euaa162.371.

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Abstract Background- Identification of variants of uncertain significance (VUSs) poses relevant challenges in counseling and managing patients. They have an unknown impact on health, making the genetic tests clinically irrelevant. Recent studies demonstrate that a routine reclassification analysis enables to reclassify from 20% to 80% of this type of variant, improving risk stratification. Purpose- We investigated whether, in the context of inherited cardiac conditions, a review of the updated literature, including new functional data, allele frequency (GnomAD) and segregation analysis may help
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