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Analysis of frequency of a RHD1227A allele in Chinese Hans.

Xiaoying WU ; Dazhou WU ; Manni WANG ; Chaopeng SHAO ; Hua XU

Chinese Journal of Medical Genetics.2014;31(6):793-796. doi:10.3760/cma.j.issn.1003-9406.2014.06.026

OBJECTIVETo determine the frequency of RHD1227A allele in Chinese Hans.

METHODSFor a total of 890403 ethnic Han blood donors, the D antigen was determined with a saline method and indirect antiglobulin test. The RHD1227A allele and number and type of zygosity of RHD gene were determined with PCR sequence specific primer (PCR-SSP). Allelic frequency was calculated through statistics.

RESULTSIn total 2385 donors were found to be Rh-negative, 108 individuals were found to be weakly positive for D antigen (including weak D and partial D phenotypes). The remaining 887 910 individuals were Rh-positive. Among the Rh-negative individuals, 516 were found with RHD1227A. Among these, 467 were RHD1227A/d and 49 were RHD1227A/RHD1227A. Two of 108 D antigen weak-positive individuals were found as RHD1227A/RHD+. In addition, 8 of 1073 random Rh-positive samples were found to be RHD1227A/RHD+. The allele frequency of RHD1227A in the population was calculated as 0.004 036. The figure should be 0.006 682 if calculated based on the detected rate of the allele in Rh-negative individuals, and 0.007 884 if calculated based on the reported average phenotype rate of DEL in Rh-negative individuals.

CONCLUSIONBy taking main influencing factors such as the RHD zygosity, the rate of RHD1227A and DEL phenotype may be determined. The allele frequency of RHD1227A in Chinese Hans is between 0.004 036 and 0.007 884.

Adolescent ; Adult ; Asian Continental Ancestry Group ; ethnology ; genetics ; China ; ethnology ; Exons ; Female ; Gene Frequency ; Genotype ; Humans ; Male ; Middle Aged ; Mutation, Missense ; Rh-Hr Blood-Group System ; genetics ; Young Adult

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Nucleotide sequence analysis for a new HLA-B allele HLA-B*13:01:06*.

Baiyu XIONG ; Yin TAN ; Yingfeng HUANG ; Shaoyu YANG ; Hongtu LUO ; Liang SHEN ; Taichen ZHOU ; Cangjun XIAO

Chinese Journal of Medical Genetics.2014;31(6):790-792. doi:10.3760/cma.j.issn.1003-9406.2014.06.025

OBJECTIVETo confirm a new allele HLA-B*13:01:06 and analyze its nucleotide sequence.

METHODSGenomic DNA was extracted using a Qiagen DNA extraction kit. Nucleotide sequences of HLA-A, HLA-B, HLA-C and HLA-DRB1 were analyzed by polymerase chain reaction-sequence based typing (PCR-SBT). HLA high-resolution results were assigned, and the nucleotide sequences of HLA-B locus was compared with that of HLA-B*13:01:01.

RESULTSThe nucleotide sequence of the new allele shows a strong similarity to that of HLA-B*13:01:01. One nucleotide in exon 2 has changed from G to A at position 219 (codon 49 GCG>GCA), which however did not result in amino acid change.

CONCLUSIONThe novel allele verified by sequencing has been submitted to GenBank and officially named as HLA-B*13:01:06 by the World Health Organization HLA Nomenclature Committee.

Alleles ; Amino Acid Sequence ; Base Sequence ; Exons ; HLA-B Antigens ; genetics ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Sequence Analysis, DNA

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Molecular genetic analysis of a weak D phenotype.

Fengqiu LIN ; Xu ZHANG ; Jianping LI

Chinese Journal of Medical Genetics.2014;31(6):786-789. doi:10.3760/cma.j.issn.1003-9406.2014.06.024

OBJECTIVETo explore the molecular basis for an individual with a rare weak D phenotype.

METHODSSerological methods were used to characterize the RhD blood group phenotype. The exons of RHD gene were amplified with PCR and sequenced. The presence of Rhesus box was tested by PCR to determine the homozygosity of RHD gene.

RESULTSThe RhD blood group of the proband was detected as weak D. The 10 exons of the RHD gene and Rhesus box could be amplified by PCR, and the genotype of RHD alleles was determined as RHD+/RHD-. The exons of the RHD gene were sequenced, and a 365C>T mutation in exon 3 was detected. Therefore, the RhD blood group of the proband was confirmed as weak D type 54 by both serological methods and DNA sequencing.

CONCLUSIONA weak D type 54 has been detected. A 365C>T mutation in RHD gene is responsible for the low expression of D antigen.

Alleles ; Base Sequence ; Exons ; Genotype ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Phenotype ; Point Mutation ; Rh-Hr Blood-Group System ; genetics

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Analysis of linkage disequilibrium and linkage for 12 short tandem repeat loci on chromosome X.

Qiansu YE ; Jianpin TANG ; Zucong CHEN ; Fagui LI ; Xin YU ; Ping WANG ; Hanguang LIN ; Meisen SHI

Chinese Journal of Medical Genetics.2014;31(6):782-785. doi:10.3760/cma.j.issn.1003-9406.2014.06.023

OBJECTIVETo analyze linkage disequilibrium of 12 short tandem repeat loci on chromosome X (X-STR) among an ethnic Han population from Guilin, Guangxi, and to study the genetic linkage and haplotype distributions of such loci in 2 linkage groups.

METHODS12 X-STR loci including DXS8378, DXS10159, DXS10162, DXS10164, DXS981, DXS6789, DXS7424, DXS101, DXS7133, GATA165B12, GATA31E08 and DXS7423 were genotyped using an AGCU X12 STR PCR Amplification kit. A total of 119 pedigrees were analyzed for linkage and linkage disequilibrium.

RESULTSTwo mutations were found at DXS7424, and 1 mutation was found at DXS10164. A total of 93 haplotypes of DXS10159-DXS10162-DXS10164 were constructed for 261 unrelated males and females, in addition with 167 haplotypes of DXS6789-DXS7424-DXS101-DXS7133. The values of recombination fraction between DXS10159 and DXS10162, DXS10162 and DXS10164, DXS6789 and DXS7424, and DXS7424 and DXS101 were 0.0269, 0.0236, 0.0505 and 0.0438, respectively.

CONCLUSIONLinkage disequilibrium of X-STR does not only depend on physical and genetic distances. There was incomplete linkage relationship between loci on DXS10159-DXS1016-DXS10164 and DXS6789-DXS7424-DXS101 linkage groups.

Adolescent ; Adult ; Asian Continental Ancestry Group ; ethnology ; genetics ; Child ; Child, Preschool ; China ; ethnology ; Chromosomes, Human, X ; genetics ; Female ; Haplotypes ; Humans ; Linkage Disequilibrium ; Male ; Microsatellite Repeats ; Middle Aged ; Pedigree ; Young Adult

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Analysis of two false positive cases from noninvasive prenatal testing.

Xuejiao CHEN ; Meizhen DAI ; Weiwu SHI ; Yingqiu PAN ; Weiguo ZHANG ; Yang ZHANG ; Zhiqiang WU

Chinese Journal of Medical Genetics.2014;31(6):778-781. doi:10.3760/cma.j.issn.1003-9406.2014.06.022

OBJECTIVETo track and analyze two false positive cases from non-invasive prenatal testing for potential fetal aneuploidy.

METHODSThe two cases, respectively reported to have XO (+++) and T18 (1/20) XO(+), were analyzed with conventional karyotyping, fluorescence in situ hybridization (FISH) and massively parallel genomic sequencing (MPS).

RESULTSThe first fetus, who was suspected for XO(+++), was verified to have super female syndrome (47,XXX/46,XX) due to confined placental mosaicism by karyotyping of amniotic fluid cells, FISH analysis of placenta and massively parallel sequencing (MPS) of fetal tissue. The second fetus, suspected to have trisomy 18 (1/20) XO(+), was verified to have Turner syndrome by karyotyping, FISH and MPS analyses of umbilical cord blood cells. And the karyotype was 45,X[48]/46, X, der(X) del(X) (p11.21) del(X) (q13.3)[62].

CONCLUSIONNon-invasive prenatal testing carries a risk for false positive diagnosis of fetal sex chromosome and trisomy 18. Combined cytogenetic and molecular techniques are required to ensure an accurate diagnosis.

Adult ; Aneuploidy ; Chromosome Aberrations ; Diagnostic Errors ; False Positive Reactions ; Female ; Fetal Diseases ; diagnosis ; genetics ; Humans ; Pregnancy ; Prenatal Diagnosis ; Young Adult

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Analysis of genomic copy number variation for a Chinese patient with split hand/split foot malformation.

Yunying CHEN ; Huanzheng LI ; Shaohua TANG ; Ting HU ; Jicheng DU

Chinese Journal of Medical Genetics.2014;31(6):774-777. doi:10.3760/cma.j.issn.1003-9406.2014.06.021

OBJECTIVETo employ single nucleotide polymorphisms (SNP) microarray to detect copy number variations (CNVs) for the diagnosis of disease and molecular classification.

METHODSFor a patient with split-hand/split-foot malformation, genome-wide copy number variants SNP microarray was applied. Tiny copy number variations were verified by real-time fluorescent quantitative PCR.

RESULTSThe results of SNP microarray has revealed that the patient has carried a 0.39 Mb duplication in 10q24.31-24.32 (102 955 122-103 348 688), which has encompassed genes including LBX1, BTRC and POLL. By real-time fluorescent quantitative PCR, duplicate area encompassing the pathogenic genes have been verified. The results for LBX1, BTRC, POLL genes were all consistent with the SNP microarray test. Moreover, a duplication was detected in exon 9 of FBXW4 gene which is in nearby.

CONCLUSIONSNP chips can efficiently identify tiny CNVs (< 1.0 Mb). In combination with real-time fluorescence quantitative PCR, this may provide valuable information for prenatal diagnosis.

Adult ; Asian Continental Ancestry Group ; genetics ; China ; Chromosome Duplication ; DNA Copy Number Variations ; DNA Polymerase beta ; genetics ; Homeodomain Proteins ; genetics ; Humans ; Limb Deformities, Congenital ; genetics ; Male ; Polymorphism, Single Nucleotide ; Transcription Factors ; genetics ; beta-Transducin Repeat-Containing Proteins ; genetics

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Gene diagnosis for a child with tuberous sclerosis.

Yan ZHANG ; Hongke DING ; Aihua YIN ; Xiaozhuang ZHANG

Chinese Journal of Medical Genetics.2014;31(6):770-773. doi:10.3760/cma.j.issn.1003-9406.2014.06.020

OBJECTIVETo identify the pathogenic mutation in a family affected with tuberous sclerosis.

METHODSFor the proband and its parents, mutational hotspots in the 11 exons of TSC1 and TSC2 gene were analyzed with DNA sequencing and bioinformatics tools.

RESULTSA heterozygous c.4493G>C missense mutation was identified in the proband. The same mutation was however not found in the parents.

CONCLUSIONThe missense mutation c.4493G>C probably underlie the tuberous sclerosis complex seen in the child.

Base Sequence ; Child ; DNA Mutational Analysis ; Exons ; Female ; Humans ; Molecular Sequence Data ; Point Mutation ; Tuberous Sclerosis ; genetics ; Tumor Suppressor Proteins ; genetics

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Studies on the association of single nucleotide polymorphisms of HLA-DP and DQ genes with the outcome of chronic hepatitis B virus infection.

Mingkuan SU ; Yongbin ZENG ; Jing CHEN ; Ling JIANG ; Tianbin CHEN ; Can LIU ; Bin YANG ; Qishui OU

Chinese Journal of Medical Genetics.2014;31(6):765-769. doi:10.3760/cma.j.issn.1003-9406.2014.06.019

OBJECTIVETo investigate the association of single nucleotide polymorphisms in the HLA-DP and DQ genes with the outcome of chronic hepatitis B virus infection.

METHODSTwo hundred and four healthy subjects, 255 clearance subjects, 204 asymptomatic HBV carriers (AsC), 136 chronic hepatitis B (CHB), 68 liver cirrhosis (LC) and hepatocellular carcinoma (HCC) were enrolled. Genotypes of rs3077, rs9277535 and rs2647050 were determined by sequence specific primers-PCR (PCR-SSP).

RESULTSBy using healthy subjects and clearance subjects as the control groups, rs3077 and rs9277535 were significantly associated with chronic HBV infection under additive and dominant models (P< 0.05). Meanwhile, haplotypes GGA, AGA, AAA appeared to be protective factors against chronic HBV infection (P < 0.05). By using AsC as the control group, comparison with the CHB, LC and HCC groups showed no association of the 3 SNPs or haplotypes with the clinical outcome (P > 0.05).

CONCLUSIONHLA-DP gene polymorphisms are strongly associated with chronic HBV infection. The presence of A allele at rs3077 and rs9277535 of the HLA-DP gene may decreased the risk for chronic HBV infection.

Adult ; Asian Continental Ancestry Group ; ethnology ; genetics ; Case-Control Studies ; China ; ethnology ; Female ; Genotype ; HLA-DP Antigens ; genetics ; HLA-DQ Antigens ; genetics ; Hepatitis B virus ; physiology ; Hepatitis B, Chronic ; ethnology ; genetics ; virology ; Humans ; Male ; Middle Aged ; Polymorphism, Single Nucleotide

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Analysis of a infertile female with ring 21 chromosome using combined techniques.

Hao WANG ; Yan WANG ; Lingfeng WU ; Lesi XIE

Chinese Journal of Medical Genetics.2014;31(6):761-764. doi:10.3760/cma.j.issn.1003-9406.2014.06.018

OBJECTIVETo investigate clinical phenotype and genetic characteristics of a 30-year-old infertile female carrying a mosaic ring 21 chromosome.

METHODSA combination of techniques including G-banding, C-banding, fluorescence in situ hybridization (FISH) and SNP array were performed to investigate the breaking point of the r(21).

RESULTSThe karyotype of the patient was mos 46,XX,r(21)[166]/46, XX,der(21)[60]/45, XX, -21[20]/46, XX,dic r(21)[4].ish del(21)(q22.2?)(21qter-, AML1+, D21S259/D21S341/D21S342+). arr 21q22.3(43 457 934-48 093 361) × 1, 21q22.2q22.3(40 218 429-43 457 934)× 1-2. The karyotypes of her parents were both normal.

CONCLUSIONClinical phenotypes of patients carrying a ring 21 mainly depends on the percentage of abnormal cells and the deleted chromosomal fragment. The small uterus and oligomenorrhea in our patient may be attributed to the mosaic ring 21 chromosome.

Adult ; Chromosome Banding ; Chromosome Deletion ; Chromosomes, Human, Pair 21 ; genetics ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Infertility, Female ; diagnosis ; genetics ; Karyotyping ; Ring Chromosomes

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Analysis of APC gene mutation in a familial adenomatous polyposis pedigree.

Min ZHANG ; Zhihong WANG ; Yanhong LIN ; Yuxiang LIN ; Xiaoli LI ; Aizhen YAN ; Xianguo FU ; Fuchun ZHONG ; Fenghua LAN

Chinese Journal of Medical Genetics.2014;31(6):757-760. doi:10.3760/cma.j.issn.1003-9406.2014.06.017

OBJECTIVETo analyze mutation of adenomatous polyposis coli (APC) gene in a family affected with familial adenomatous polyposis.

METHODSThe diagnosis was made based on clinical manifestations, family history, presence of numerous polyps in the colon as well as pathological examination. Peripheral blood samples were collected, and genomic DNA was extracted. Potential mutation of the APC gene was detected by polymerase chain reaction (PCR) and DNA sequencing. After finding the mutation in the proband, the same mutation was screened among other family members. The mutation was also confirmed with PCR-restriction fragment length polymorphism (RFLP), with which 100 unrelated healthy controls were examined.

RESULTSA novel heterozygous nonsense mutation c.2891T>G (L964X) of the APC gene was identified in this pedigree. The mutation has led to premature termination of translation. The same mutation was not detected among the 100 healthy controls.

CONCLUSIONThe c.2891T>G (L964X) of the APC gene probably underlies the familial adenomatous polyposis in this pedigree. The combined DNA sequencing and PCR-RFLP method is efficient and accurate for the diagnosis.

Adenomatous Polyposis Coli ; diagnosis ; genetics ; Adenomatous Polyposis Coli Protein ; genetics ; Adult ; Base Sequence ; Child, Preschool ; Colorectal Neoplasms ; diagnosis ; genetics ; Female ; Humans ; Male ; Molecular Sequence Data ; Mutation, Missense ; Pedigree ; Point Mutation ; Young Adult

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