Donor cell chimerism evaluation in cerebrospinal fluid by short tandem repeat analysis following allogeneic hematopoietic stem cell transplantation

Cerebrospinal fluid (CSF) cell count, morphology and flow cytometric evaluations are used to investigate central nervous system (CNS) involvement in leukemia/lymphoma. We performed CSF short tandem repeat (STR) analysis to monitor CSF chimerism status and evaluate for disease involvement in 11 asymptomatic pediatric allogeneic hematopoietic stem cell transplantation (HSCT) recipients with hemato-lymphoid neoplasms and high risk for or history of CNS involvement. Eighteen (64%) of the samples with median CSF cell count of 1/mm³ with 90% lymphocytes gave conclusive STR results, suggesting that this DNA-based method can be used in monitoring CSF chimerism status after HSCT with an acceptable yield.     

Biallelic mutations in DYNC2LI1 are a rare cause of Ellis‐van Creveld syndrome

Ellis‐van Creveld syndrome (EvC) is a chondral and ectodermal dysplasia caused by biallelic mutations in the EVC, EVC2 and WDR35 genes. A proportion of cases with clinical diagnosis of EvC, however, do not carry mutations in these genes. To identify the genetic cause of EvC in a cohort of mutation‐negative patients, exome sequencing was undertaken in a family with 3 affected members, and mutation scanning of a panel of clinically and functionally relevant genes was performed in 24 additional subjects with features fitting/overlapping EvC. Compound heterozygosity for the c.2T>C (p.Met1?) and c.662C>T (p.Thr221Ile) variants in DYNC2LI1, which encodes a component of the intraflagellar transport‐related dynein‐2 complex previously found mutated in other short‐rib thoracic dysplasias, was identified in the 3 affected members of the first family. Targeted resequencing detected compound heterozygosity for the same missense variant and a truncating change (p.Val141*) in 2 siblings with EvC from a second family, while a newborn with a more severe phenotype carried 2 DYNC2LI1 truncating variants. Our findings indicate that DYNC2LI1 mutations are associated with a wider clinical spectrum than previously appreciated, including EvC, with the severity of the phenotype likely depending on the extent of defective DYNC2LI1 function.     

Clinical sequencing: From raw data to diagnosis with lifetime value

High‐throughput sequencing (HTS) has revolutionized genetics by enabling the detection of sequence variants at hitherto unprecedented large scale. Despite these advances, however, there are still remaining challenges in the complete coverage of targeted regions (genes, exome or genome) as well as in HTS data analysis and interpretation. Moreover, it is easy to get overwhelmed by the plethora of available methods and tools for HTS. Here, we review the step‐by‐step process from the generation of sequence data to molecular diagnosis of Mendelian diseases. Highlighting advantages and limitations, this review addresses the current state of (1) HTS technologies, considering targeted, whole‐exome, and whole‐genome sequencing on short‐ and long‐read platforms; (2) read alignment, variant calling and interpretation; as well as (3) regulatory issues related to genetic counseling, reimbursement, and data storage.     

The role of inhibition for working memory processes: ERP evidence from a short‐term storage task

Human working memory is the central unit for short‐term storage of information. In addition to the selection and adequate storage of relevant information, the suppression of irrelevant stimuli from the environment seems to be of importance for working memory processes. To learn more about the interplay of information uptake and inhibition of irrelevant information, the present study used ERP measures and a short‐term storage and retrieval task, in which pairs of either numbers or letters had to be compared. Random sequences of four stimuli (two numbers and two letters) were presented, with either the numbers or the letters being relevant for comparison. The analysis of ERPs to each of the four stimuli indicated more pronounced P2 and P3b amplitudes for relevant than irrelevant stimuli. In contrast, the N2 (reflecting inhibitory control) was only elicited by irrelevant stimuli. Moreover, the N2 amplitude of the second irrelevant stimulus was associated with behavioral performance, indicating the importance of inhibition of task‐irrelevant stimuli for working memory processes. In sum, the findings demonstrate the role of cognitive control mechanisms for protecting relevant contents in working memory against irrelevant information.     

Nomenclature for factors of the HLA system, update May 2009

Major histocompatibility complex class I chain-related gene A ( MICA ) is located 46 kb centromeric to HLA-B locus and encodes a stress-inducible protein. MICA allelic variation is thought to be associated with disease susceptibility and immune response to transplants. In this study, polymerase chain reaction sequence-based typing (PCR-SBT) method for MICA alleles has been established. Genomic DNAs from 100 healthy Chinese Han individuals were typed for MICA alleles by this method. The microsatellite polymorphism in the exon 5 of MICA gene, MICA * Del allele, and human leukocyte antigen-B alleles was also detected by the polymerase chain reaction–GeneScan, polymerase chain reaction sequence-specific primer, and PCR-SBT methods, respectively. Fourteen MICA alleles were found in the population, with MICA * 00801/04 having the highest frequency of 27.0%. MICA * A4 , * A5 , * A5.1 , * A6 , and * A9 microsatellites were identified. Two samples with HLA-B * 4801 were MICA * Del positive, with the frequency of 1.0%. The data showed that the new PCR-SBT method for MICA alleles was reliable and Chinese Han population was distinct in distribution of MICA alleles.     

广西毛南族17个Y染色体短串联重复序列基因座遗传多态性

目的:调查17个Y染色体短串联重复序列(Y-STR)基因座及其单倍型在广西毛南族人群中的分布情况.方法:应用AmpFlSTR YfilerTM荧光标记复合扩增系统,对毛南族208名无关男性个体血样进行17个Y-STR位点的复合扩增,用ABI PRISM310遗传分析仪对扩增产物进行检测分析.结果:DYS456、 DYS389Ⅰ、 DYS390、 DYS389Ⅱ、 DYS458、 DYS19、 DYS385a＼b、 DYS393、 DYS391、 DYS439、 DYS635、 DYS392、 Y-GATA-H4、 DYS437、 DYS438、 DYS448各位点遗传多样性(GD值)分布在0 5852～0 9770之间.17个Y-STR位点共同构成的单倍型205种,其单倍型多样性为0 999785.广西毛南族与其他群体的Y-STR位点等位基因分布差异具有统计学意义.结论:广西毛南族17个Y-STR位点具有丰富的遗传多样性,可为父权鉴定和父系进化研究提供有价值的遗传学资料.     

Copy number variants in patients with short stature

Height is a highly heritable and classic polygenic trait. Recent genome-wide association studies (GWAS) have revealed that at least 180 genetic variants influence adult height. However, these variants explain only about 10% of the phenotypic variation in height. Genetic analysis of short individuals can lead to the discovery of novel rare gene defects with a large effect on growth. In an effort to identify novel genes associated with short stature, genome-wide analysis for copy number variants (CNVs), using single-nucleotide polymorphism arrays, in 162 patients (149 families) with short stature was performed. Segregation analysis was performed if possible, and genes in CNVs were compared with information from GWAS, gene expression in rodents'' growth plates and published information. CNVs were detected in 40 families. In six families, a known cause of short stature was found (SHOX deletion or duplication, IGF1R deletion), in two combined with a de novo potentially pathogenic CNV. Thirty-three families had one or more potentially pathogenic CNVs (n=40). In 24 of these families, segregation analysis could be performed, identifying three de novo CNVs and nine CNVs segregating with short stature. Four were located near loci associated with height in GWAS (ADAMTS17, TULP4, PRKG2/BMP3 and PAPPA). Besides six CNVs known to be causative for short stature, 40 CNVs with possible pathogenicity were identified. Segregation studies and bioinformatics analysis suggested various potential candidate genes.     

西藏昌都藏族15个短串联重复序列基因座的遗传多样性

的分布特点.用ARLEQUIN 3.0软件计算等位基因频率和各种多态性参数.结果 西藏昌都藏族群体中15个STR位点上观察到135个等位基因,等位基因频率分布在0.0065～0.5455之间;平均杂合度为0.7340,个体识别力除了TPOX(0.7927)和TH01(0.7919)外均大于0.8,累计个体识别力为0.9999998,累计非父排除率为0.99999997.结论 西藏昌都藏族15个STR位点均具有高度遗传多态性,是群体遗传学研究和法医学鉴定的可选位点.