BACKGROUND: Single-nucleotide polymorphisms (SNPs)-associated genes and long non-coding RNAs (lncRNAs) can contribute to human disease. To comprehensively investigate the contribution of lncRNAs to breast cancer, we performed the first genome-wide lncRNA association study on Han Chinese women. METHODS: We designed an lncRNA array containing >800,000 SNPs, which was incorporated into a 96-array plate by Affymetrix (CapitalBio Technology, China). Subsequently, we performed a two-stage genome-wide lncRNA association study on Han Chinese women covering 11,942 individuals (5634 breast cancer patients and 6308 healthy controls). Additionally, in vitro gain or loss of function strategies were performed to clarify the function of a novel SNP-associated gene. RESULTS: We identified a novel breast cancer-associated susceptibility SNP, rs11066150 (Pmeta = 2.34 × 10-8), and a previously reported SNP, rs9397435 (Pmeta = 4.32 × 10-38), in Han Chinese women. rs11066150 is located in NONHSAT164009.1 (lncHSAT164), which is highly expressed in breast cancer tissues and cell lines. lncHSAT164 overexpression promoted colony formation, whereas lncHSAT164 knockdown promoted cell apoptosis and reduced colony formation by regulating the cell cycle. CONCLUSIONS Based on our lncRNA array, we identified a novel breast cancer-associated lncRNA and found that lncHSAT164 may contribute to breast cancer by regulating the cell cycle. These findings suggest a potential therapeutic target in breast cancer.
Asian Continental Ancestry Group/genetics* ; Breast Neoplasms/genetics* ; Case-Control Studies ; China ; Female ; Genetic Predisposition to Disease/genetics* ; Genome-Wide Association Study ; Humans ; Polymorphism, Single Nucleotide/genetics* ; RNA, Long Noncoding/genetics*

Asian Continental Ancestry Group/genetics* ; BRCA1 Protein/genetics* ; China ; Consensus ; Humans

OBJECTIVE: To explore the clinical characteristics and genetic basis for a pair of twins affected with hyaline fibromatosis syndrome (HFS). METHODS: Clinical data of the twins were retrospectively analyzed. High-throughput sequencing was carried out to detect potential pathogenic variants. CLUSTALX was employed to analyze cross-species conservation of the mutant amino acids. Impact of the mutations was predicted by using software including PolyPhen-2 and Mutation taster. RESULTS: The pair of twins have featured growth and intelligence retardation, and were found to carry compound heterozygous variants of the ANTXR2 gene including c.1214G>A and c.1074delT, among which c.1214G>A was unreported previously. Both variants were predicted to be pathogenic. In addition to growth and mental delay, the pair of twins also featured hyperplasia of the gum and soft tissue-like masses of the auricle. The younger brother had rupture of the auricle mass during follow-up. CONCLUSION The patients' condition can probably be attributed to the compound heterozygous variants of the ANTXR2 gene. Above finding has facilitated molecular diagnosis of the patients.
Asian Continental Ancestry Group/genetics* ; China ; Humans ; Hyalinosis, Systemic/genetics* ; Male ; Mutation ; Pedigree ; Receptors, Peptide/genetics* ; Retrospective Studies

OBJECTIVE: To investigate the genetic polymorphisms of 21 non-combined DNA index system short tandem repeat (STR) loci in Hainan Li population. METHODS: DNA samples from 339 unrelated healthy individuals of Li population from Hainan Province were extracted and amplified with fluorescence labeled multiplex PCR system. PCR products were electrophoresed on an ABI3130 Genetic Analyzer following the manufacturer's instructions. Allele designation was performed with a GeneMapper ID-X by comparison with the allele ladder provided by the corresponding kit. RESULTS: A total of 173 alleles and 489 genotypes were observed for the 21 STR loci, respectively. The frequencies of alleles and genotypes were 0.0010-0.5434 and 0.0020-0.3274, respectively. The heterozygosity varied from 0.639 to 0.833. Discrimination power (DP) was 0.803-0.948, power of exclusion for trio-paternity was 0.416-0.584, power of exclusion for duo-paternity was 0.140-0.238, the polymorphism information content(PIC) was 0.57-0.81, respectively. The total discrimination power (TDP), cumulative probability of exclusion for trio-paternity testing(CPE-trio) and cumulative probability of exclusion for duo-paternity testing (CPE-duo) were 0.999 999 999 999 99, 0.999 999 883 211 752, and 0.987 266, respectively. CONCLUSION The 21 STR loci are highly polymorphic and informative in the studied population and can be employed as supplementary loci in duo-paternity testing or cases with variant circumstances.
Asian Continental Ancestry Group/genetics* ; China ; DNA ; Gene Frequency ; Genetics, Population ; Humans ; Microsatellite Repeats/genetics* ; Polymorphism, Genetic

Asian Continental Ancestry Group ; BRCA1 Protein/genetics* ; Breast Neoplasms/surgery* ; China ; Female ; Genetic Testing ; Humans ; Mastectomy

OBJECTIVES: Due to the genetic feature of high diversity than other DNA markers, short tandem repeat (STR) plays key roles in forensic, anthropology, and population genetics. Newly introduced multiple STR kit is more valuable because of the greatly improved discriminatory power with the increase in the number of STR loci. The genetic polymorphic data are essential for the application and research in specific population. This study aims to investigate the genetic polymorphism of Han population residing in Yuncheng district, Shanxi Province, to evaluate the application of 23 STR loci in forensic personal identification and paternity test, and to explore the genetic relationship of Han population between Yuncheng and other populations. METHODS: A total of 23 STR loci were amplified from 525 healthy unrelated individuals from the Han nationality in Yuncheng, Shanxi Province using the AGCU EX25 amplification kit. The products were detected and separated by ABI 3500 Genetic Analyzer. Alleles were genotyped by GeneMapper ID (Version 3.2) software, and corresponding frequencies and forensic parameters were calculated. We calculated the genetic distance and plotted the neighboring-joining tree with other 13 population. RESULTS: The allele frequency of the 23 STRs ranged from 0.0010 to 0.5090. No deviation from Hardy-Weinberg equilibrium ( CONCLUSIONS These 23 STRs are highly genetic polymorphic and informative in the Han population of Yuncheng, Shanxi Province, which can provide basic data for forensic personal identification, paternity testing, and population genetic research.
Asian Continental Ancestry Group/genetics* ; China ; Ethnic Groups/genetics* ; Gene Frequency ; Genetic Loci ; Genetics, Population ; Humans ; Microsatellite Repeats/genetics* ; Polymorphism, Genetic

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.
Amyotrophic Lateral Sclerosis/genetics* ; Asian Continental Ancestry Group ; Heat-Shock Proteins ; Heterozygote ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Chaperones ; Phenotype

OBJECTIVE: To detect potential variant in an ethical Han Chinese pedigree affected with breast cancer. METHODS: The proband and her relatives were subjected to next-generation sequencing using a target capture sequencing kit containing 121 cancer-related genes. Candidate variants were selected by analysis of their type, frequency in population, and segregation with the phenotype. Candidate variant was verified by Sanger sequencing and TA cloning. RESULTS: A c.2013_2014ins GT variant was detected in the BRCA1 gene among all breast cancer patients from this pedigree but not among healthy females. The variant was not recorded in the 1000 Genome Project database or the Exome Aggregation Consortium (ExAC) database. The frameshifting insertion was predicted to form an premature stop codon in gene transcript and can give rise to a truncated protein. CONCLUSION The BRCA1 c.2013_2014ins GT variant probably underlies the pathogenesis of breast cancer in this Chinese pedigree.
Asian Continental Ancestry Group ; BRCA1 Protein ; genetics ; Breast Neoplasms ; genetics ; Exome ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Pedigree ; Phenotype

OBJECTIVE: To explore the molecular etiology for a Chinese family with mitochondrial DNA depletion syndrome. METHODS: Genomic DNA was extracted from peripheral blood samples of the patient and her parents.Targeted capture and next-generation sequencing was carried out to detect potential variants. Suspected variant was validated by Sanger sequencing. RESULTS: A novel homozygous frameshift variant c.505_508delTATC was identified in the patient, for which both his mother and father were carriers. CONCLUSION The frameshift variant c.505_508delTATC probably underlies the mitochondrial DNA depletion syndrome in this patient. The result also enriched the variant spectrum of DGUOK gene.
Asian Continental Ancestry Group ; genetics ; DNA, Mitochondrial ; genetics ; Female ; Frameshift Mutation ; Humans ; Mutation ; Phosphotransferases (Alcohol Group Acceptor) ; genetics ; Syndrome

A case of Gilbert syndrome (GS) with a heterozygous mutation in the gene is reported. The patient had no symptoms except for recurrent sclera icterus since childhood. Laboratory examinations revealed an elevated unconjugated bilirubin. Biliary obstruction, hemolysis and other diseases that might cause jaundice were excluded. *28 and c.211G>A heterozygous mutations in gene were found, which may be another type of mutation causing GS in Chinese population.
Asian Continental Ancestry Group ; Bilirubin ; Gilbert Disease ; genetics ; Glucuronosyltransferase ; genetics ; Heterozygote ; Humans ; Mutation