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BMC Medical Genomics Jun 2024Distal hereditary motor neuropathy (dHMN) is a heterogeneous group of hereditary diseases caused by the gradual degeneration of the lower motor neuron. More than 30...
BACKGROUND
Distal hereditary motor neuropathy (dHMN) is a heterogeneous group of hereditary diseases caused by the gradual degeneration of the lower motor neuron. More than 30 genes associated with dHMN have been reported, while 70-80% of those with the condition are still unable to receive a genetic diagnosis.
METHODS
A 26-year-old man experiencing gradual weakness in his lower limbs was referred to our hospital, and data on clinical features, laboratory tests, and electrophysiological tests were collected. To identify the disease-causing mutation, we conducted whole exome sequencing (WES) and then validated it through Sanger sequencing for the proband and his parents. Silico analysis was performed to predict the pathogenesis of the identified mutations. A literature review of all reported mutations of the related gene for the disease was performed.
RESULTS
The patient presented with dHMN phenotype harboring a novel homozygous variant c.361G > C (p.Ala121Pro) in SORD, inherited from his parents, respectively. A121 is a highly conserved site and the mutation was categorized as "likely pathogenic" according to the criteria and guidelines of the American College of Medical Genetics and Genomics (ACMG). A total of 13 published articles including 101 patients reported 18 SORD variants. Almost all described cases have the homozygous deletion variant c.757delG (p.A253Qfs*27) or compound heterozygous state of a combination of c.757delG (p.A253Qfs*27) with another variant. The variant c.361G > C (p.Ala121Pro) detected in our patient was the second homozygous variant in SORD-associated hereditary neuropathy.
CONCLUSION
One novel homozygous variant c.361G > C (p.Ala121Pro) in SORD was identified in a Chinese patient with dHMN phenotype, which expands the mutation spectrum of SORD-associated hereditary neuropathy and underscores the significance of screening for SORD variants in patients with undiagnosed hereditary neuropathy patients.
Topics: Humans; Male; Adult; Mutation; Exome Sequencing; Hereditary Sensory and Motor Neuropathy; Pedigree; Phenotype
PubMed: 38915017
DOI: 10.1186/s12920-024-01940-5 -
Thrombosis and Haemostasis Jun 2024Venous thromboembolism (VTE) is predisposed by thrombotic mutations in patients with hereditary thrombophilia. Although prothrombin deficiencies caused by homozygous or...
BACKGROUND
Venous thromboembolism (VTE) is predisposed by thrombotic mutations in patients with hereditary thrombophilia. Although prothrombin deficiencies caused by homozygous or compound heterozygous mutations are associated with bleeding diathesis, rare cases have shown a correlation between heterozygous prothrombin mutations and thrombosis.
MATERIAL AND METHODS
We surveyed genetic variants involved in thrombosis and hemostasis in 347 patients with unprovoked VTE or having a positive family history of thrombosis. For patients identified with heterozygous prothrombin mutations, we conducted family investigations and performed thrombin generation test (TGT) to elucidate the thrombotic risk. Novel mutants were expressed and subjected to functional assays to clarify the underlying thrombotic mechanisms.
RESULTS
Heterozygous prothrombin mutations were identified in 3.5% of patients (12/347), including three novel mutations Phe382Ser, Phe382Leu and Asp597Tyr found in one patient each, as well as previously reported Arg541Trp mutation in four patients and Arg596Gln mutation in five patients. A total of 42 mutation carriers were identified within the 12 pedigrees, among whom 64.3% (27/42) had experienced thrombotic events. TGT results demonstrated hypercoagulability for carriers of the five mutations, with Arg596Gln showing the highest thrombin generation potential followed by Arg541Trp. The Phe382-associated mutations severely impaired thrombomodulin binding ability of thrombin, resulting in obviously reduced protein C (PC) activation. The Asp597Tyr mutation exhibited a mild reduction in both antithrombin inhibition and PC activation reactions.
CONCLUSIONS
The presence of heterozygous prothrombin mutations represents a potential genetic predisposition for VTE. All thrombosis associated mutations potentiate coagulation activity by either conferring antithrombin resistance and/or impairing PC pathway activity.
PubMed: 38914130
DOI: 10.1055/a-2350-8338 -
Proceedings of the National Academy of... Jul 2024The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the...
The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.
Topics: Humans; History, Medieval; Pedigree; Belgium; Burial; Genetics, Population; Female; Male; DNA, Ancient; England; Human Migration; Archaeology; Netherlands; Genome, Human
PubMed: 38913897
DOI: 10.1073/pnas.2406734121 -
PeerJ 2024Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a...
Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population's genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performed with the competitive allele-specific PCR genotyping method on 36 horses belonging to all sire lines. The analysis of the mtDNA hypervariable region detected 47 SNPs, which assigned all tested horses to 43 haplotypes. Most dam lines presented more than one haplotype; however, five dam lines were represented by only one haplotype. The haplotypes were classified into six (A, B, E, J, G, R) recognized mtDNA haplogroups, with most horses belonging to haplogroup A, common among Asian horse populations. Y chromosome analysis allocated Polish Koniks in the Crown group, condensing all modern horse breeds, and divided them into three haplotypes clustering with coldblood breeds (28 horses), warmblood breeds (two horses), and Duelmener Pony (six horses). The clustering of all Wicek sire line stallions with Duelmener horses may suggest a historical relationship between the breeds. Additionally, both mtDNA and Y chromosome sequence variability results indicate crossbreeding before the studbooks closure or irregularities in the pedigrees occurred before the DNA testing introduction.
Topics: Animals; Horses; DNA, Mitochondrial; Poland; Y Chromosome; Haplotypes; Male; Polymorphism, Single Nucleotide; Female; Breeding
PubMed: 38912049
DOI: 10.7717/peerj.17549 -
Molecular Genetics and Metabolism... Sep 2024The detailed clinical phenotype of patients carrying the α-galactosidase gene () / () variant in Fabry disease (FD) has not been thoroughly documented in the...
BACKGROUND
The detailed clinical phenotype of patients carrying the α-galactosidase gene () / () variant in Fabry disease (FD) has not been thoroughly documented in the existing literature.
METHODS
This paper offers a meticulous overview of the clinical phenotype and relevant auxiliary examination results of nine confirmed FD patients with the gene variant from two families. Pedigree analysis was conducted on two male patients with the gene variant, followed by biochemical and genetic screening of all high-risk relatives. Subsequently, evaluation of multiple organ systems and comprehensive instrument assessment were performed on heterozygotes of the gene variant.
RESULTS
The study revealed that all patients exhibited varying degrees of cardiac involvement, with two demonstrating left ventricular wall thickness exceeding 15 mm on echocardiography, and the remaining six exceeding 11 mm. Impaired renal function was evident in all six patients with available blood test data, two of whom underwent kidney transplantation. Eight cases reported neuropathic pain, and five experienced varying degrees of stroke or transient ischemic attack (TIA).
CONCLUSION
This study indicates that the gene variant can induce premature organ damage, particularly affecting the heart, kidneys, and nervous system.
PubMed: 38911695
DOI: 10.1016/j.ymgmr.2024.101102 -
Dementia and Geriatric Cognitive... 2024Microglia exert a crucial role in homeostasis of white matter integrity, and several studies highlight the role of microglial dysfunctions in neurodegeneration. Primary...
INTRODUCTION
Microglia exert a crucial role in homeostasis of white matter integrity, and several studies highlight the role of microglial dysfunctions in neurodegeneration. Primary microgliopathy is a disorder where the pathogenic abnormality of the microglia causes white matter disorder and leads to a neuropsychiatric disease. Triggering receptor expressed on myeloid cells (), TYRO protein tyrosine kinase binding protein () and colony-stimulating factor 1 receptor () are genes implicated in primary microgliopathy. The clinical manifestations of primary microgliopathy are myriad ranging from neuropsychiatric syndrome, motor disability, gait dysfunction, ataxia, pure dementia, frontotemporal dementia (FTD), Alzheimer's dementia (AD), and so on. It becomes imperative to establish the diagnosis of microgliopathy masquerading as degenerative dementia, especially with promising therapies on horizon for the same. We aimed to describe a case series of subjects with dementia harbouring novel genes of primary microgliopathy, along with their clinical, neuropsychological, cognitive profile and radiological patterns.
METHODS
The prospective study was conducted in a university referral hospital in South India, as a part of an ongoing clinico-genetic research on dementia subjects, and was approved by the Institutional Ethics Committee. All patients underwent detailed assessment including sociodemographic profile, clinical and cognitive assessment, pedigree analysis and comprehensive neurological examination. Subjects consenting for blood sampling underwent genetic testing by whole-exome sequencing (WES).
RESULTS
A total of 100 patients with dementia underwent genetic analysis using WES and three pathogenic variants, one each of , , and and two variants of uncertain significance in were identified as cause of primary microgliopathy. and presented as frontotemporal syndrome whereas CSF1R presented as frontotemporal syndrome and as AD.
CONCLUSION
WES has widened the spectrum of underlying neuropathology of degenerative dementias, and diagnosing primary microglial dysfunction with emerging therapeutic options is of paramount importance. The cases of primary microgliopathy due to novel mutations in , , and with the phenotype of degenerative dementia are being first time reported from Indian cohort. Our study enriches the spectrum of genetic variants implicated in degenerative dementia and provides the basis for exploring complex molecular mechanisms like microglial dysfunction, as underlying cause for neurodegeneration.
PubMed: 38910897
DOI: 10.1159/000538145 -
Molecular Genetics and Genomics : MGG Jun 2024Familial Hypophosphatasia presents a complex diagnostic challenge due to its wide-ranging clinical manifestations and genetic heterogeneity. This study aims to elucidate...
Familial Hypophosphatasia presents a complex diagnostic challenge due to its wide-ranging clinical manifestations and genetic heterogeneity. This study aims to elucidate the molecular underpinnings of familial Hypophosphatasia within a Tunisian family harboring a rare c.896 T > C mutation in the ALPL gene, offering insights into genotype-phenotype correlations and potential therapeutic avenues. The study employs a comprehensive approach, integrating biochemical examination, genetic analysis, structural modeling, and functional insights to unravel the impact of this rare mutation. Genetic investigation revealed the presence of the p.Leu299Pro mutation within the ALPL gene in affected family members. This mutation is strategically positioned in proximity to both the catalytic site and the metal-binding domain, suggesting potential functional consequences. Homology modeling techniques were employed to predict the 3D structure of TNSALP, providing insights into the structural context of the mutation. Our findings suggest that the mutation may induce conformational changes in the vicinity of the catalytic site and metal-binding domain, potentially affecting substrate recognition and catalytic efficiency. Molecular dynamics simulations were instrumental in elucidating the dynamic behavior of the tissue-nonspecific alkaline phosphatase isozyme (TNSALP) in the presence of the p.Leu299Pro mutation. The simulations indicated alterations in structural flexibility near the mutation site, with potential ramifications for the enzyme's overall stability and function. These dynamic changes may influence the catalytic efficiency of TNSALP, shedding light on the molecular underpinnings of the observed clinical manifestations within the Tunisian family. The clinical presentation of affected individuals highlighted significant phenotypic heterogeneity, underscoring the complex genotype-phenotype correlations in familial Hypophosphatasia. Variability in age of onset, severity of symptoms, and radiographic features was observed, emphasizing the need for a nuanced understanding of the clinical spectrum associated with the p.Leu299Pro mutation. This study advances our understanding of familial Hypophosphatasia by delineating the molecular consequences of the p.Leu299Pro mutation in the ALPL gene. By integrating genetic, structural, and clinical analyses, we provide insights into disease pathogenesis and lay the groundwork for personalized therapeutic strategies tailored to specific genetic profiles. Our findings underscore the importance of comprehensive genetic and clinical evaluation in guiding precision medicine approaches for familial Hypophosphatasia.
Topics: Humans; Hypophosphatasia; Male; Female; Alkaline Phosphatase; Pedigree; Tunisia; Adult; Molecular Dynamics Simulation; Catalytic Domain; Mutation; Genetic Association Studies; Middle Aged
PubMed: 38909345
DOI: 10.1007/s00438-024-02157-y -
Journal of Dairy Science Jun 2024This study explores how the metafounder (MF) concept enhances genetic evaluations in dairy cattle populations using single-step genomic best linear unbiased prediction...
This study explores how the metafounder (MF) concept enhances genetic evaluations in dairy cattle populations using single-step genomic best linear unbiased prediction (ssGBLUP). By improving the consideration of relationships among founder populations, MF ensures accurate alignment of pedigree and genomic relationships. The research aims to propose a method for grouping MF based on genotypic information, assess different approaches for estimating the gamma matrix, and compare unknown parent groups (UPG) and MF methodologies across various scenarios, including those with low and high pedigree completeness based on a simulated dairy cattle population. In the scenario where unknown ancestors are rare, the impact of UPG or MF on breeding values is minimal but MF still performs slightly better compared with UPG. The scenario with lower genotyping rates and more unknown parents shows significant differences in evaluations with and without UPG and also compared with MF. The study shows that ssGBLUP evaluations where UPG are considered via Quaas-Pollak-transformation in the pedigree-based and genomic relationship matrix (UPG_fullQP) results in double counting and subsequently in a pronounced bias and overdispersion. Another focus is on the estimation of the gamma matrix, emphasizing the importance of crossbred genotypes for accuracy. Challenges emerge in classifying animals into subpopulations and further into MF or UPG, but the method used in this study, which is based on genotypes, results in predictions which are comparable to those obtained using the true subpopulations for the assignment. Estimated validation results using the linear regression method confirm the superior performance of MF evaluations, although differences compared with true validations are smaller. Notably, UPG_fullQP's extreme bias is less evident in routine validation statistics.
PubMed: 38908687
DOI: 10.3168/jds.2024-24891 -
Transfusion Clinique Et Biologique :... Jun 2024
PubMed: 38908507
DOI: 10.1016/j.tracli.2024.06.006 -
Methods in Molecular Biology (Clifton,... 2024The outcome of Hematopoietic Stem Cell (HSCT) and organ transplant is strongly affected by the matching of the HLA alleles of the donor and the recipient. However,...
The outcome of Hematopoietic Stem Cell (HSCT) and organ transplant is strongly affected by the matching of the HLA alleles of the donor and the recipient. However, donors and sometimes recipients are often typed at low resolution, with some alleles either missing or ambiguous. Thus, imputation methods are required to detect the most probably high-resolution HLA haplotypes consistent with a typing. Such imputation algorithms require predefined haplotype frequencies. As such, the phasing of the typing is required for both imputation and frequency generation.We have developed a new approach to HLA haplotype and genotype imputation, where first all candidate phases of a typing are explicated, and then the ambiguity within each phase is solved. This ambiguity is solved through a graph structure of all partial haplotypes and the haplotypes consistent with them.This phasing approach was used to produce an imputation algorithm (GRIMM-Graph Imputation and Matching). GRIMM was then combined with the possibility of combining information from multiple races to produce MR-GRIMM (Multi-Race GRIMM). When family information is available, the phasing of each family member can be restricted by the others. We propose GRAMM (GRaph-bAsed faMily iMputation) to phase alleles in family pedigree HLA typing data and in mother-cord blood unit pairs. Finally, we combined MR-GRIMM with an expectation-maximization (EM) algorithm to estimate haplotype frequencies sharing information between races to produce MR-GRIMME (MR-GRIMM EM).We have shown that these algorithms naturally combine information between races and family members. The accuracy of each of these algorithms is significantly better than its current parallel methods. MR-GRIMM leads to high accuracy in matching predictions. GRAMM better imputes family members than either MR-GRIMM or any existing algorithm and has practically no phasing errors. MR-GRIMME obtains a higher likelihood than existing algorithms.MR-GRIMM, MR-GRIMME, and GRAMM are available as servers or through stand-alone versions in GITHUB and PyPi, as detailed in the appropriate sections.
Topics: Humans; Haplotypes; Algorithms; HLA Antigens; Histocompatibility Testing; Tissue Donors; Alleles; Software; Gene Frequency; Family; Genotype; Hematopoietic Stem Cell Transplantation
PubMed: 38907899
DOI: 10.1007/978-1-0716-3874-3_13