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2.
Article in Chinese | WPRIM | ID: wpr-879627

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a child featuring global developmental delay.@*METHODS@#DNA was extracted from peripheral blood sample taken from the patient and subjected to whole exome sequencing. Suspected variants were verified by Sanger sequencing of his family members.@*RESULTS@#A heterozygous c.239T>C (p.Ile80Thr) variant of the GNB1 gene was detected in the proband, which was a verified to be de novo in origin.@*CONCLUSION@#The heterozygous c.239T>C (p.Ile80Thr) variant of the GNB1 gene probably underlay the disease in this child.


Subject(s)
Arthrogryposis , Child , Family , GTP-Binding Protein beta Subunits , Heterozygote , Humans , Intellectual Disability/genetics , Whole Exome Sequencing
3.
Article in Chinese | WPRIM | ID: wpr-879623

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a pedigree affected with hereditary multiple osteochondroma (HMO).@*METHODS@#Peripheral blood samples were collected from the proband and members of his pedigree with informed consent. Following extraction of genomic DNA, all coding exons and flanking intronic sequences (-10 bp) of the EXT1 and EXT2 genes were subjected to targeted capture and next generation sequencing (NGS). Suspected variant was verified by Sanger sequencing.@*RESULTS@#A heterozygous nonsense variant (c.1911C>A) was found in exon 10 of the EXT1 gene in the proband and his affected father but not in a healthy sister and normal controls. The variant was classified as a pathogenic based on the guidelines of the American College of Medical Genetics and Genomics (PVS1+PM2+PP1). Bioinformatic analysis predicted that the c.1911C>A variant may be disease-causing via nonsense-mediated mRNA decay and anomalous splicing.@*CONCLUSION@#The c.1911C>A variant probably underlay the disease in this pedigree. Discovery of this variant enriched the variant spectrum of HMO.


Subject(s)
Codon, Nonsense , Exons/genetics , Exostoses, Multiple Hereditary/genetics , Heterozygote , Humans , Pedigree
4.
Article in Chinese | WPRIM | ID: wpr-879622

ABSTRACT

OBJECTIVE@#To explore the genetic basis of a pedigree affected with Alagille syndrome (ALGS).@*METHODS@#Targeted capture and next generation sequencing was carried out for the proband. Candidate variants were verified by Sanger sequencing among his family members. Their pathogenicity of the variant was predicted with bioinformatic analysis. Clinical characteristics and genotype-phenotype correlation were analyzed.@*RESULTS@#The proband, his elder sister and mother were found to carry a heterozygous c.1270dupG (p.Ala424Glyfs*5) variant of the JAG1 gene, which may lead to premature termination of translation and a truncated protein with loss of function. The variant was unreported previously. The phenotypes of the proband (cholestasis, pulmonary artery stenosis and peculiar faces) have differed from those of his elder sister (cholestasis with pruritus, posterior embryonic ring of cornea) and mother (with no clinical manifestation). Cholestasis and peculiar face of the proband became insignificant with age.@*CONCLUSION@#The c.1270dupG (p.Ala424Glyfs*5) variant of the JAG1 gene probably underlay the ALGS in this pedigree with incomplete penetrance.


Subject(s)
Aged , Alagille Syndrome/genetics , Heterozygote , High-Throughput Nucleotide Sequencing , Humans , Pedigree , Phenotype
5.
Article in Chinese | WPRIM | ID: wpr-879606

ABSTRACT

OBJECTIVE@#To explore the genetic variation of a Chinese family affected with congenital insensitivity to pain with anhidrosis and albinism.@*METHODS@#Whole exome sequencing (WES) was carried out to screen potential variants within genomic DNA extracted from the proband and his parents. Whole genome sequencing (WGS) was applied when variants were not found completely. Suspected variants were validated by Sanger sequencing.@*RESULTS@#WES has identified a heterozygous c.1729G>C (p.G577R) variant of NTRK1 gene and two heterozygous variants of OCA2 gene, namely c.1363A>G (p.R455G) and c.1182+1G>A. WGS has identified two additional heterozygous variants c.(851-798C>T; 851-794C>G) in deep intronic regions of the NTRK1 gene.@*CONCLUSION@#The compound heterozygous variants of the NTRK1 gene probably underlay the congenital insensitivity to pain with anhidrosis. And the compound heterozygous variants of the OCA2 gene probably underlay the albinism in the proband. In the case where no variant is detected by WES in the coding region, WGS should be considered to screen potential variants in the whole genome.


Subject(s)
Albinism , Child , DNA Mutational Analysis , Hereditary Sensory and Autonomic Neuropathies/genetics , Heterozygote , Humans , Membrane Transport Proteins , Mutation , Pedigree
6.
Article in Chinese | WPRIM | ID: wpr-879601

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a Chinese pedigree affected with non-syndromic hearing loss (NSHL).@*METHODS@#Commercialized gene chip was applied to detect common mutations associated with congenital deafness. Whole exome sequencing was carried out for patients for whom gene chip yielded a negative result. Candidate variants were verified by Sanger sequencing.@*RESULTS@#Two patients from the pedigree were discovered to carry compound heterozygous variants of the TRIOBP gene, namely c.3299C>A and c.5185-2A>G. Their parents had normal hearing and were both heterozygous carriers of the above variants. Both variants had co-segregated with the disease phenotype in the pedigree and were unreported previously.@*CONCLUSION@#Pathogenic variants of the TRIOBP gene comprise an important factor for NSHL. The novel c.5185-2A>G and c.3299C>A variants discovered in this study have enriched the mutational spectrum of the TRIOBP gene and enabled molecular diagnosis and genetic counseling for the family.


Subject(s)
Deafness/genetics , Hearing Loss, Sensorineural/genetics , Heterozygote , Humans , Microfilament Proteins/genetics , Mutation , Pedigree , Whole Exome Sequencing
7.
Article in Chinese | WPRIM | ID: wpr-879588

ABSTRACT

OBJECTIVE@#To describe the clinical and genetic characteristics of a child with 14q12q13.1 deletion involving the FOXG1 gene.@*METHODS@#Clinical manifestation of the child was analyzed. Peripheral blood sample of the patient was subjected to chromosomal karyotyping and single nucleotide polymorphism array (SNP-array) analysis.@*RESULTS@#The male infant has developed feeding difficulty, poor sucking, lower limb tremor, and frontal bruising 8 days after birth. Magnetic resonance imaging revealed significant enlargement of bilateral ventricles and corpus callosum dysplasia. Chromosomal analysis revealed a karyotype of 46,XY,del(14)(q12q13.1), and SNP-array confirmed that there was a 9.6 Mb deletion in 14q11.2q13.1, which encompassed the FOXG1 gene.@*CONCLUSION@#For patients with brain development abnormalities, dyskinesia, cognitive impairment, speech disorder and other manifestations, copy number variation of the FOXG1 gene should be excluded. SNP-array should be carried out as early as possible to attain the diagnosis.


Subject(s)
Child , Chromosome Deletion , DNA Copy Number Variations , Forkhead Transcription Factors/genetics , Heterozygote , Humans , Infant , Karyotyping , Male , Nerve Tissue Proteins/genetics , Polymorphism, Single Nucleotide
8.
Article in Chinese | WPRIM | ID: wpr-879570

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a child affected with Bainbridge-Ropers syndrome.@*METHODS@#Genomic DNA was extracted from peripheral venous blood samples from the patient and his parents. Whole exome sequencing (WES) was carried out to detect genetic variant of the proband. Candidate variant was verified by Sanger sequencing.@*RESULTS@#The 3-year-old boy presented with psychomotor retardation, linguistic difficulties, mental retardation and peculiar craniofacial phenotype. A de novo heterozygous nonsense variant of the ASXL3 gene, c.3106C>T, was identified by WES in the proband, and the same mutation was not found among his parents. Based on the American College of Medical Genetics and Genomics standards and guidelines, the c.3106C>T variant was predicted to be pathogenic (PVS1+PS2+PP4).@*CONCLUSION@#The heterozygous variant c.3106C>T of the ASXL3 gene probably underlies the Bainbridge-Ropers syndrome in the patient. Above result has enabled the clinical diagnosis and genetic counseling for the family.


Subject(s)
Child , Child, Preschool , Heterozygote , Humans , Intellectual Disability/genetics , Male , Mutation , Phenotype , Transcription Factors/genetics , Whole Exome Sequencing
9.
Article in Chinese | WPRIM | ID: wpr-879562

ABSTRACT

OBJECTIVE@#To analyze the clinical phenotype and genetic basis for a Chinese pedigree affected with coagulation factor XI (FXI) deficiency.@*METHODS@#Activated partial thromboplastin time (APTT) and other blood coagulation factors, and activities of FXI:C and other relevant coagulation factors for a large Chinese pedigree including 6 patients from 3 generations were determined on a Stago automatic coagulometer. The FXI:Ag was determined with an ELISA method. All exons and flanking regions of the F11 gene were subjected to Sanger sequencing. ClustalX-2.1-win software was used to analyze the conservation of amino acids. Pathogenicity of the variants was predicted with online bioinformatics software including Mutation Taster and Swiss-Pdb Viewer.@*RESULTS@#The APTT of the proband was prolonged to 94.2 s. The FXI:C and FXI:Ag were decreased to 1% and 1.3%, respectively. The APTT of her father, mother, son and daughter was 42.1 s, 43.0 s, 42.5 s and 41.0 s, respectively. The FXI:C and FXI:Ag of them were almost halved compared with the normal values. The APTT, FXI:C and FXI:Ag of her husband were all normal. Genetic testing revealed that the proband has carried a heterozygous missense c.1103G>A (p.Gly350Glu) variant in exon 10 and a heterozygous missense c.1556G>A (p.Trp501stop) variant in exon 13 of the F11 gene. The father and daughter were heterozygous for the c.1103G>A variant, whilst the mother and son were heterozygous for the c.1556G>A variant. Both Gly350 and Trp501 are highly conserved among homologous species, and both variants were predicted to be "disease causing" by Mutation Taster. Protein modeling indicated there are two hydrogen bonds between Gly350 and Phe312 in the wild-type, while the p.Gly350Glu variant may add a hydrogen bond to Glu and Tyr351 and create steric resistance between the two, both may affect the structure and stability of protein.@*CONCLUSION@#The c.1103G>A and c.1556G>A compound heterozygous variants probably underlay the pathogenesis of congenital FXI deficiency in this pedigree.


Subject(s)
Exons/genetics , Factor XI/genetics , Factor XI Deficiency/genetics , Female , Heterozygote , Humans , Male , Mutation , Pedigree
10.
Article in Chinese | WPRIM | ID: wpr-879556

ABSTRACT

OBJECTIVE@#To carry out prenatal diagnosis for families with high risk for spinal muscular atrophy (SMA) by using multiplex ligation-dependent probe amplification (MLPA).@*METHODS@#Twenty-one families were enrolled. MLPA was used to detect copy numbers of SMN1 and SMN2 genes. Maternal contamination was excluded by using a short tandem repeat method.@*RESULTS@#For 23 fetuses from the 21 families, 14 were identified as carriers, 1 as SMA patient, and 8 as normal. By linkage analysis of parental samples, three individuals were determined as silent (2+0) carriers.@*CONCLUSION@#MLPA can determine the carrier status of SMA. The identification of three silent (2+0) carriers among the 44 parental samples indicated a risk for such families, for which genetic counseling and reproduction guidance should be provided.


Subject(s)
Female , Genetic Counseling , Heterozygote , Humans , Multiplex Polymerase Chain Reaction , Muscular Atrophy, Spinal/genetics , Pregnancy , Prenatal Diagnosis , Survival of Motor Neuron 1 Protein/genetics
11.
Article in Chinese | WPRIM | ID: wpr-879551

ABSTRACT

OBJECTIVE@#To explore the genetic basis of a pedigree affected with peroneal muscular atrophy.@*METHODS@#Neuroelectrophysiological examination and whole exome sequencing were carried out for the proband, a six-year-and-ten-month-old boy. Suspected variant was verified in his family members through Sanger sequencing. Bioinformatic analysis was carried to predict the conservation of amino acid sequence and impact of the variant on the protein structure and function.@*RESULTS@#Electrophysiological examination showed demyelination and axonal changes of motor and sensory nerve fibers. A heterozygous missense c.1066A>G (p. Thr356Ala) variant was found in exon 11 of the MFN2 gene in the proband and his mother, but not in his sister and father. Bioinformatic analysis using PolyPhen-2 and Mutation Taster software predicted the variant to be pathogenic, and that the sequence of variation site was highly conserved among various species. Based no the American College of Medical Genetics and Genomics standards and guidelines, the c.1066A>G (p. Thr356Ala) variant of MFN2 gene was predicted to be likely pathogenic (PS1+ PM2+ PP3+ PP4).@*CONCLUSION@#The heterozygous missense c.1066A>G (p.Thr356Ala) variant of the MFN2 gene probably underlay the disease in the proband, and the results have enabled genetic counseling and prenatal diagnosis for this family.


Subject(s)
Charcot-Marie-Tooth Disease/genetics , Child , China , Drosophila Proteins/genetics , Exons , Female , Heterozygote , Humans , Male , Membrane Proteins/genetics , Mutation , Pedigree , Pregnancy , Whole Exome Sequencing
12.
Article in Chinese | WPRIM | ID: wpr-879543

ABSTRACT

OBJECTIVE@#To analyze the clinical features, biochemical characteristics and molecular pathogenesis of a girl with isovaleric acidemia.@*METHODS@#Clinical features, blood spot amino acid profiles and urinary organic acid profiles of the patient were analyzed. Targeted capture, next generation sequencing and Sanger sequencing were carried out to detect potential variant of the IVD gene.@*RESULTS@#The patient presented with poor weight gain, poor feeding, lethargy, and a "sweaty feet" odor 10 days after birth. Biochemical test suggested hyperammonemia. Blood spot amino acid profiles displayed a dramatic increase in isovalerylcarnitine (C5: 3. 044, reference range 0.04 - 0.4 μmol/L). Organic acid analysis of her urine sample revealed a high level of isovaleric glycine (669. 53, reference range 0 - 0.5). The child was ultimately diagnosed with isovaleric acidemia, and was found to harbor a paternally derived heterozygous variant c.149G>A (p.R50H) and a maternally derived heterozygous variant c.1123G>A (p.G375S) of the IVD gene. Her elder brother was a heterozygous carrier of c.1123G>A (p.G375S) variant. The c.149G>A (p.R50H) was a known pathogenic variant, while the c.1123G>A (p.G375S) variant was previously unreported.@*CONCLUSION@#The pathogenesis of the patient was delineated from the perspective of genetics, which has provided a basis for clinical diagnosis, treatment as well as genetic counseling.


Subject(s)
Amino Acid Metabolism, Inborn Errors/genetics , Child , Female , Heterozygote , Humans , Isovaleryl-CoA Dehydrogenase/genetics , Male , Mutation
13.
Article in Chinese | WPRIM | ID: wpr-879538

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a patient with intellectual disability.@*METHODS@#Whole exome sequencing and Sanger sequencing were carried out for the patient. The result was verified in her family.@*RESULTS@#DNA sequencing revealed that the patient has carried a heterozygous nonsense c.40C>T (p.Arg14X) variant of the TRIP12 gene, which was de novo in origin. The variant was unrecorded in the Human Gene Mutation Database. Based on the American College of Medical Genetics and Genomics standards and guidelines, the variant was predicted to be pathogenic (PVS1+ PS2+ PP3).@*CONCLUSION@#The patient was diagnosed with autosomal dominant intellectual disability due to heterozygous c.40C>T variant of the TRIP12 gene.


Subject(s)
Carrier Proteins/genetics , Codon, Nonsense , Female , Heterozygote , Humans , Intellectual Disability/genetics , Ubiquitin-Protein Ligases/genetics , Whole Exome Sequencing
14.
Article in Chinese | WPRIM | ID: wpr-879537

ABSTRACT

OBJECTIVE@#To analyze the clinical phenotype and genetic characterization of a child with early infantile epileptic encephalopathy.@*METHODS@#The proband was subjected to history taking and was diagnosed based on his clinical manifestation, magnetic resonance imaging (MRI) and whole exome sequencing (WES). Sanger sequencing was carried out to determine the origin of pathogenic variant.@*RESULTS@#The proband unconsciously tilts his head to one side with squint, which revealed an abnormal discharge. MRI indicated suspicious abnormal signal shadow in the left posterior frontal cortex in addition with inflammation signs in the right maxillary sinus and ethmoid sinus. WES revealed that the proband has carried a heterozygous c.5789G>A variant in the CACNAIA gene. The result of Sanger sequencing was in keeping with that of WES. Neither of his parents has carried the same variant.@*CONCLUSION@#The heterozygous c.5789G>A variant of the CACNAIA gene probably underlay the early infantile epileptic encephalopathy 42 in the proband, which has a de novo origin.


Subject(s)
Calcium Channels/genetics , Genetic Testing , Heterozygote , Humans , Infant , Mutation , Spasms, Infantile/genetics , Whole Exome Sequencing
15.
Article in Chinese | WPRIM | ID: wpr-879529

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a fetus with hydrocephalus.@*METHODS@#The fetus was found to have hydrocephalus upon ultrasonography duringthe second trimester. Following induced abortion, fetal tissue was collected for the extraction of DNA and whole exome sequencing.Sanger sequencing was used to verify the suspected variants in the family.@*RESULTS@#The fetus was found to harbor a hemizygous c.620A>G (p.Tyr207Cys) variant of the L1CAM gene (OMIM 308840),for which his mother and sister were heterozygous carriers. The same variant was not found in his father, uncle and grandparents.Based on the standards and guidelines of the American College of Medical Genetics and Genomics, the variant was predicted to be likely pathogenic (PM1+PM2+PP3+PP4).@*CONCLUSION@#The hemizygous c.620A>G (p.Tyr207Cys) variant of the L1CAM gene probably underlay the hydrocephalus in this fetus.


Subject(s)
Adult , Female , Heterozygote , Humans , Hydrocephalus/genetics , Male , Mutation , Neural Cell Adhesion Molecule L1/genetics , Pedigree , Pregnancy , Whole Exome Sequencing
16.
Article in Chinese | WPRIM | ID: wpr-879511

ABSTRACT

OBJECTIVE@#To analyze the hematological phenotypes of Hb J-Bangkok and concomitant thalassemia.@*METHODS@#In total 72 397 samples were screened by using capillary electrophoresis. Samples with Hb J-Bangkok were identified by DNA sequencing and analysis of red blood cell parameters. Gap-PCR and PCR-reverse dot blotting (PCR-RDB) were used for analyzing the thalassemia genes.@*RESULTS@#Thirty one cases of Hb J-Bangkok were identified, all of which were heterozygotes. The hematological phenotype index (Hb, mean corpuscular volume, mean corpuscular hemoglobin, Hb J-Bangkok, Hb A@*CONCLUSION@#Hb J-Bangkok heterozygotes have normal hematological phenotypes, though they may show different hematological characteristics when concomitant with different types of thalassemia, for which genetic counseling should be provided accordingly.


Subject(s)
Female , Hemoglobins, Abnormal/genetics , Heterozygote , Humans , Male , Phenotype , Thailand , beta-Thalassemia/genetics
17.
Article in Chinese | WPRIM | ID: wpr-880830

ABSTRACT

OBJECTIVE@#To explore the association between rare HSPB1 variants and amyotrophic lateral sclerosis (ALS).@*METHODS@#We performed next-generation sequencing for 166 Chinese ALS patients to screen for possible pathogenic rare variants of HSPB1. The control individuals were obtained from 1000 Genome Project and an in-house whole-exome sequencing database. The Sequence Kernel Association Test (SKAT) and the SKAT-optimal test (SKAT-O) were used to identify the association between rare HSPB1 variants and ALS.@*RESULTS@#We identified 3 possible pathogenic rare variants of HSPB1 (all were missenses), including c.379C>T (p.R127W), c.446A>C (p.D149A) and c.451A>C (p.T151P). Compared with 1000 Genome Project, SKAT p=3.61×10@*CONCLUSIONS@#Rare variants of HSPB1 are probably associated with the pathogenesis of ALS.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , Asian Continental Ancestry Group , Heat-Shock Proteins , Heterozygote , High-Throughput Nucleotide Sequencing , Humans , Molecular Chaperones , Phenotype
18.
Article in Chinese | WPRIM | ID: wpr-880159

ABSTRACT

OBJECTIVE@#To analyze the gene defect types and distribution characteristics of α- and β-thalassemia in Lingui District of Guilin City, Guangxi, so as to provide scientific basis for genetic consultation and prevention measures.@*METHODS@#A total of 6 496 suspected cases for screening the thalassemia during physical examination, premarital examination, pregnancy examination and hospitalization in the Second Affiliated Hospital of Guilin Medical University from May 2016 to October 2019 were analyzed. Gap-PCR, PCR-RDB and DNA sequencing techniques were used to detect the types and constituent ratios of gene defects in α- and β-thalassemia positive cases.@*RESULTS@#Among 6 496 suspected patients, 1 363 were thalassemia carriers, the total positive rate was 20.98%. There were 677 cases of single-gene deletion and 26 cases of double-gene detetion on the deletional α-thalassemia, 115 cases of non-deletion α-thalassemia mutation and 4 cases of deletion plus mutation. The positive rate of α-thalassemia was 12.66%. There were 11 gene abnormalities for α-thalassemia, of which --@*CONCLUSION@#Lingui district of Guilin city is a high incidence area of thalassemia. The mutation rate of α-thalassemia --


Subject(s)
China/epidemiology , Female , Genotype , Heterozygote , Humans , Mutation , Pregnancy , alpha-Thalassemia/genetics , beta-Thalassemia/genetics
19.
Article in Chinese | WPRIM | ID: wpr-880119

ABSTRACT

OBJECTIVE@#To detecte the carrying rate, the type and distribution of α-Thalassemia gene mutation in Honghe Prefecture, Yunnan Province, and analyze the differences in average erythrocyte volume (MCV), mean erythrocyte hemoglobin content (MCH) and hemoglobin among different types of α-Thalassemia.@*METHODS@#The DNA samples from small cell hypochromic carriers or anemia patients and women of childbearing age who underwent hematological screening in The First People's Hospital of Honghe State was from 2015 to 2019 were enrolled and analyzed, and the mutation types and frequency of alpha-thalassemia positive rate were diagnosed by PCR reverse dot blot or PCR fluorescence dissolution curve.@*RESULTS@#Among the 1 016 samples, 141(13.88%) of the patients were diagnosed as α-thalassemia. The α-thalassemia was subdivided into 3 types, silent (36.17%), minor (51.77%), and HbH disease (12.06%), and the MCV, MCH and HB levels were detected and showed a obvious decrease trend with significant difference (P < 0.05). The gene mutation types were 9 kinds, the deletion type gene was mainly --SEA (51.06%), followed by -α@*CONCLUSION@#Alpha-thalassemia in Honghe prefecture of Yunnan Province shows complex genetic diversity and significant genetic heterogeneity, and the mainly type of gene mutation is --SEA and --


Subject(s)
China , Female , Genotype , Heterozygote , Humans , Mutation , alpha-Thalassemia/genetics , beta-Thalassemia
20.
Article in Chinese | WPRIM | ID: wpr-880118

ABSTRACT

OBJECTIVE@#To test the anticoagulation functions, perform the genetic diagnosis and analyze the clinical characteristics in a family with combined heterozygous genetic variants of PROC and PROS1.@*METHODS@#Peripheral blood was collected from all the family members. Hematological phenotypes and activity of anticoagulant factors were analyzed. Target genes were amplified by PCR from DNA isolated from peripheral blood, and then were analyzed by Sanger DNA sequencing.@*RESULTS@#Many members in the family displayed the combined genetic variants in protein C and protein S, and six family members accompanied by deep venous thrombosis (DVT). The influences of genetic and secondary factors on the incidence of venous thrombosis in the family members were analyzed. The results showed that in this family, carriers of combined protein C and protein S gene defects had a higher incidence of VTE, but acquired factors still played a key role in the eventual thrombotic symptoms.@*CONCLUSION@#Venous thromboembolism (VTE) is a multifactorial disease, the combined genetic heterozygous mutations of protein C and S is an important genetic factor, and the clinical phenotype show a high heterogenicity, the secondary factors contribute to the VTE incidence.


Subject(s)
Heterozygote , Humans , Mutation , Protein C/genetics , Protein S/genetics , Risk Factors , Venous Thromboembolism , Venous Thrombosis/genetics
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