检索结果-内蒙古大学图书馆

Impact of snp microarray analysis of compromised DNA on kinship classification success in the context of investigative genetic genealogy

引用

FORENSIC SCIENCE INTERNATIONAL-GENETICS 2022年第0期56卷 102625-102625页

作者： de Vries, Jard H. Kling, Daniel Vidaki, Athina Arp, Pascal Kalamara, Vivian Verbiest, Michael M. P. J. Piniewska-Rog, Danuta Parsons, Thomas J. Uitterlinden, Andre G. Kayser, Manfred Univ Med Ctr Rotterdam Dept Internal Med Erasmus MC Dr Molewaterpl 40 NL-3015 GD Rotterdam Netherlands Natl Board Forens Med Dept Forens Genet & Toxicol Artillerigatan 12 S-58758 Linkoping Sweden Univ Med Ctr Rotterdam Dept Genet Identificat Erasmus MC Dr Molewaterpl 40 NL-3015 GD Rotterdam Netherlands Jagiellonian Univ Malopolska Ctr Biotechnol PL-30387 Krakow Poland Jagiellonian Univ Dept Forens Med Med Coll PL-31531 Krakow Poland Int Commiss Missing Persons Koninginnegracht 12a NL-2514 AA The Hague Netherlands Univ Med Ctr Rotterdam Dept Epidemiol Erasmus MC Dr Molewaterpl 40 NL-3015 GD Rotterdam Netherlands

Single nucleotide polymorphism (snp) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, an approach referred to as investigative genetic genealogy (IGG). However, snp microarrays were developed for relatively high input DNA quantity and quality, while DNA typically obtainable from crime scene stains is of low DNA quantity and quality, and snp microarray data obtained from compromised DNA are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of snp microarray analysis of compromised DNA on kinship classification success, as relevant in IGG. Reference data from manufacturerrecommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 ng to 6.25 pg led to decreased snp call rates and increased genotyping errors, kinship classification success did not decrease down to 250 pg for siblings and 1st cousins, 1 ng for 2nd cousins, while at 25 pg and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800 to 200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false po

关键词： snp microarray Investigative genetic genealogy Relative identification Kinship classification Compromised DNA Forensic genetics

来源：评论

学校读者我要写书评

暂无评论

Investigation of Yersinia pestis and Yersinia pseudotuberculosis strains from Georgia and neighboring countries in the Caucasus by high-density snp microarray

引用

ARCHIVES OF MICROBIOLOGY 2018年第9期200卷 1345-1355页

作者： Zhgenti, Ekaterine Hu, Ping Chanturia, Gvantsa Tsereteli, David Kekelidze, Merab Chubinidze, Svetlana Zangaladze, Ekaterine Imnadze, Paata Andersen, Gary Torok, Tamas Natl Ctr Dis Control & Publ Hlth NCDC Georgia M Asatiani St 9 GE-0186 Tbilisi Georgia Lawrence Berkeley Natl Lab 1 Cyclotron RdMailstop 70A3317 Berkeley CA 94720 USA Ilia State Univ Ctr Pathogen Res & Educ Tbilisi Georgia

Yersinia pestis, the causative agent of plague, is a recently evolved clone of the enteropathogenic bacterium Yersinia pseudotuberculosis. Y. pestis has been extensively studied for decades;however, there are insufficient data about the intra-species diversity of this microorganism in certain parts of the world, including the Caucasus region. Using a high-density single-nucleotide polymorphism (snp) microarray, we genotyped a total of 46 Y. pestis isolates from two plague foci in Georgia and neighboring Caucasus countries together with 12 Y. pseudotuberculosis isolates from Georgia. The genotyping microarray captured a total of 13,525 snp positions across the Y. pestis and Y. pseudotuberculosis genomes and plasmids with high-throughput capability and superior reproducibility. From this analysis, we confirmed the presence of two independent and relatively distant phylogenetic groups of Y. pestis in the Caucasus region. The signature snp patterns identified from this study will allow assay development for plague surveillance and pseudotuberculosis diagnostics.

关键词： Y. pestis Y. pseudotuberculosis snp microarray Caucasus Georgia

来源：评论

学校读者我要写书评

暂无评论

Temple syndrome: A patient with maternal hetero-UPD14, mixed iso- and hetero-disomy detected by snp microarray typing of patient-father duos

引用

BRAIN & DEVELOPMENT 2016年第7期38卷 669-673页

作者： Shin, Eun-hye Cho, Eunhae Lee, Cha Gon Eulji Univ Dept Pediat Eulji Gen Hosp Coll Med 68 Hangeulbiseok Ro Seoul 139711 South Korea Green Cross Genome Yongin South Korea

Temple syndrome (TS, MIM 616222) is an imprinting disorder involving genes within the imprinted region of chromosome 14q32. TS is a genetically complex disorder, which is associated with maternal uniparental disomy of chromosome 14 (UPD14), paternal deletions on chromosome 14, or loss of methylation at the intergenic differentially methylated region (IG-DMR). Here, we describe the case of a patient with maternal hetero-UPD14, mixed iso-Thetero-disomy mechanism identified by a single nucleotide polymorphism (snp) array analysis of patient-father duos study. The phenotype of our case is similarities to Prader Willi syndrome (PWS) during infancy and to Russell-Silver syndrome (RSS) during childhood. This snp array appears to be an effective initial screening tool for patients with nonspecific clinical features suggestive of chromosomal disorders. (C) 2016 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

关键词： Uniparental disomy Uniparental heterodisomy Maternal Chromosome 14 Temple syndrome snp microarray

来源：评论

学校读者我要写书评

暂无评论

Identification of Chromothripsis in Biopsy Using snp-Based microarray

Identification of Chromothripsis in Biopsy Using SNP-Based M...

引用

作者： Veronica Ortega Christina Mendiola Gopalrao V. Velagaleti

One of the well-known hallmarks of cancer is genomic instability. Although gradualism is a well-established process of cancer evolution, recent studies have shown that chromothripsis or chromoanasynthesis can result in complex genomic rearrangements by a single catastrophic event rather than several incremental steps. These two novel phenomena suggest an evolutionary modality for cancer cells to circumvent individual mutational events with one simultaneous shattering of chromosomes or chromosome regions resulting in the random reassembling of shattered genetic material to form complex derivative chromosomes. Although sequencing methods are ideal for the detection of chromothripsis, single-nucleotide polymorphism (snp)-based microarray methods are also useful in detecting chromothripsis in biopsy samples. Issues related to sample collection, storage, and transport, especially with tumor biopsies, may limit the options for sequencing studies, and in such cases, snp-based microarray may be a viable alternative for detecting chromothripsis. less

关键词： snp microarray Biopsy microarray DNA Extraction Electrophoresis PCR DNA Ligation DNA Cancer Chromothripsis Copy number variants (CNVs)

来源：评论

学校读者我要写书评

暂无评论

Nonmosaic tetrasomy 15q25.2 → qter identified with snp microarray in a patient with characteristic facial appearance and review of the literature

引用

EUROPEAN JOURNAL OF MEDICAL GENETICS 2014年第7期57卷 329-333页

作者： Xu, Huihui Xiao, Bing Ji, Xing Hu, Qin Chen, Yingwei Qiu, Wenjuan Shanghai Jiao Tong Univ Sch Med Xinhua Hosp Shanghai 200092 Peoples R China Shanghai Inst Pediat Res Dept Genet Shanghai Peoples R China Shanghai Inst Pediat Res Dept Pediat Endocrinol & Genet Metab Shanghai Peoples R China

Tetrasomy for the distal chromosome 15q is rare, and only 22 patients (including 6 cases without detailed information) have been described to date in the literature. Here we report on another patient with nonmosaic tetrasomy 15q25.2-qter resulted from an inverted duplication of distal chromosome 15. This patient presents with features of development delay, arachnodactyly, joint contractures and typical facial dysmorphism including frontal bossing, short palpebral fissures, long philtrum, low-set ears, high-arched palate and retrognathia. Unlike most of the related patients, abdominal ultrasound test and brain MRI showed normal. Karyotyping analysis revealed a supernumerary marker chromosome presented in all metaphase cells examined. Parental karyotyping analysis was normal, indicating a de novo chromosome aberration of the patient. snp microarray analysis found a two copy gain of 17.7 Mb from the distal long arm of chromosome 15 (15q25.2-qter). Further FISH analysis using SureFISH 15q26.3 IGF1R probe proved an inverted duplication of distal long arm of chromosome 15. The segmental duplications which lie in the hotspots of 15q24-26 might increase the susceptibility of chromosome rearrangement. Compared with the George-Abraham' study [2012], ADAMTSL3 might be more related to the cardiac disorders in tetrasomy 15q patients. Considering all patients reported in the literature, different mosaic degrees and segmental sizes don't correlate to the severity of phenotypes. A clear delineation on tetrasomy for distal chromosome 15q could still be investigated. (C) 2014 Elsevier Masson SAS. All rights reserved.

关键词： Nonmosaic Tetrasomy 15q Inverted duplication Supernumerary marker chromosome snp microarray ADAMTSL3

来源：评论

学校读者我要写书评

暂无评论

Diagnosis and discovery: Insights from the NIH Undiagnosed Diseases Program

引用

JOURNAL OF INHERITED METABOLIC DISEASE 2022年第5期45卷 907-918页

作者： Montano, Carolina Cassini, Thomas Ziegler, Shira G. Boehm, Manfred Nicoli, Elena-Raluca Mindell, Joseph A. Soldatos, Ariane G. Manoli, Irini Wolfe, Lynne Macnamara, Ellen F. Malicdan, May Christine, V Adams, David R. Tifft, Cynthia J. Toro, Camilo Gahl, William A. NHGRI Med Genet & Genom Med Training Program NIH Bethesda MD 20892 USA Johns Hopkins Univ Sch Med Dept Pediat Baltimore MD 21205 USA Johns Hopkins Univ Sch Med Dept Genet Med Baltimore MD USA NHLBI Lab Cardiovasc Regenerat Med NIH Bldg 10 Bethesda MD 20892 USA NHGRI Glycosphingolipid & Glycoprot Disorders Unit Med Genet Branch NIH Bethesda MD 20892 USA NINDS Membrane Transport Biophys Sect NIH Bldg 36Rm 4D04 Bethesda MD 20892 USA NINDS Off Clin Director NIH Bldg 36Rm 4D04 Bethesda MD 20892 USA NHGRI Organ Acid Res Sect NIH Bethesda MD 20892 USA NHGRI Off Clin Director NIH Bethesda MD 20892 USA NIH NIH Undiagnosed Dis Program Common Fund Bldg 10 Bethesda MD 20892 USA

Living with an undiagnosed medical condition places a tremendous burden on patients, their families, and their healthcare providers. The Undiagnosed Diseases Program (UDP) was established at the National Institutes of Health (NIH) in 2008 with the primary goals of providing a diagnosis for patients with mysterious conditions and advancing medical knowledge about rare and common diseases. The program reviews applications from referring clinicians for cases that are considered undiagnosed despite a thorough evaluation. Those that are accepted receive clinical evaluations involving deep phenotyping and genetic testing that includes exome and genomic sequencing. Selected candidate gene variants are evaluated by collaborators using functional assays. Since its inception, the UDP has received more than 4500 applications and has completed evaluations on nearly 1300 individuals. Here we present six cases that exemplify the discovery of novel disease mechanisms, the importance of deep phenotyping for rare diseases, and how genetic diagnoses have led to appropriate treatment. The creation of the Undiagnosed Diseases Network (UDN) in 2014 has substantially increased the number of patients evaluated and allowed for greater opportunities for data sharing. Expansion to the Undiagnosed Diseases Network International (UDNI) has the possibility to extend this reach even farther. Together, networks of undiagnosed diseases programs are powerful tools to advance our knowledge of pathophysiology, accelerate accurate diagnoses, and improve patient care for patients with rare conditions.

关键词： amyloidosis CHST14 CLCN7 exome sequencing KMT2B NT5E SNORD118 snp microarray Undiagnosed Diseases Program whole genome sequencing

来源：评论

学校读者我要写书评

暂无评论

A rare case of postnatal mosaic trisomy 12 with severe congenital heart disease and literature review

引用

AMERICAN JOURNAL OF MEDICAL GENETICS PART A 2021年第6期185卷 1864-1869页

作者： Hu, Xiaolin Ayala, Sofia Saenz Dyer, Lisa Guan, Qiaoning Pena, Loren Cincinnati Childrens Hosp Med Ctr Div Human Genet Cincinnati OH 45229 USA Univ Cincinnati Coll Med Dept Pediat Cincinnati OH USA

Trisomy 12 is a rare autosomal aneuploidy. All postnatally diagnosed individuals with trisomy 12 have been mosaic for this chromosome abnormality. We herein report an infant girl presented at 2 weeks of age with severe congenital heart defect, tracheobronchomalacia, and dysmorphic features. All of the dysmorphic features of this patient fit into the known phenotype spectrum of mosaic trisomy 12, although this patient uniquely presented with macrocephaly. Tracheo-bronchomalacia has been described once previously but had a significant impact on this patient's clinical course. The patient passed away at 2-month-old due to cardiac and respiratory complications. Chromosomal single nucleotide polymorphism (snp) microarray analysis on a peripheral blood sample from the patient revealed trisomy 12 in approximately 50% of cells. Concurrent fluorescence in situ hybridization analysis of uncultured blood cells detected a comparable level of trisomy 12 mosaicism. Compared to conventional cytogenetics, snp microarray examines all nucleated cells without sampling bias, has an increased power to estimate mosaicism level, and can provide a quick assessment of the underlying mechanism. Here we demonstrate the utilization of snp microarray in the clinical diagnosis of those once considered rare disorders but might have been missed by conventional cytogenetic techniques.

关键词： aneuploidy mosaic trisomy 12 snp microarray

来源：评论

学校读者我要写书评

暂无评论

Temple syndrome resulting from uniparental disomy is undiagnosed by a methylation assay due to low-level mosaicism for trisomy 14

引用

AMERICAN JOURNAL OF MEDICAL GENETICS PART A 2021年第5期185卷 1538-1543页

作者： Lindgren, Valerie Cobian, Katherine Bhat, Gifty Univ Illinois Dept Pathol Chicago IL 60612 USA Univ Illinois Dept Pediat Sect Genet Chicago IL 60612 USA

We describe a patient with Temple syndrome resulting from maternal uniparental disomy of chromosome 14 who also has low-level mosaicism for trisomy 14. UPD was initially suspected when snp microarray analysis detected a large region of homozygosity on chromosome 14 and the patient's clinical features were consistent with the phenotype of upd(14)mat. However, snp arrays cannot prove UPD, as homozygosity may also result from identity by descent. Methylation assays diagnose imprinting disorders such as Prader-Willi, Angelman and Temple syndromes;they detect methylation defects that occur in imprinted loci, which have parent-of-origin-specific expression and have the advantage of making a diagnosis without parental samples. However, in this patient methylation analysis using endpoint PCR detected biparental inheritance. Therefore, sequencing analysis was performed and diagnosed upd(14)mat. Re-examination of the microarray suggested that the explanation for the discrepancy between the array and methylation testing was low-level mosaicism for trisomy 14 and fluorescence in situ hybridization testing detected a trisomic cell line. Thus, this patient's Temple syndrome is a result of a maternal M1 error, which gave a trisomic zygote, followed by loss of the paternal chromosome 14 in an early mitotic division to give maternal UPD with low-level mosaicism for trisomy 14. The methylation assay detected the paternal allele in the trisomic line. The diagnostic failure of the methylation assay in this patient highlights a significant shortcoming of methylation endpoint analysis, especially for Temple syndrome, and underscores the need to use other methods in cases with mosaicism.

关键词： methylation assay mosaicism snp microarray Temple syndrome uniparental disomy

来源：评论

学校读者我要写书评

暂无评论

Genetic counseling and screening of consanguineous couples and their offspring practice resource: Focused Revision

引用

JOURNAL OF GENETIC COUNSELING 2021年第5期30卷 1354-1357页

作者： Bennett, Robin L. Malleda, Neeraja R. Byers, Peter H. Steiner, Robert D. Barr, Kimberly M. Univ Washington Dept Med Div Med Genet Seattle WA 98195 USA LifeCell Int Pvt Ltd Mumbai Maharashtra India Univ Washington Dept Med Med Genet Dept Lab Med & Pathol Seattle WA USA Univ Wisconsin Prevent Genet Marshfield Clin Hlth Syst Sch Med & Publ Hlth Madison WI USA Kaiser Permanente Med Ctr Dept Genet San Francisco CA USA

There are no evidence-based guidelines to inform genetic counseling for consanguineous couples and their offspring. This focused revision builds on the expert opinions from the original publication of "Genetic Counseling and Screening of Consanguineous Couples and Their Offspring," based on a review of literature published since 2002.

关键词： consanguinity genetic counselling genetic screening genetic testing incest newborn screening snp microarray tandem mass spectrometry

来源：评论

学校读者我要写书评

暂无评论

Impact of male age on paternal aneuploidy: single-nucleotide polymorphism microarray outcomes following blastocyst biopsy

引用

REPRODUCTIVE BIOMEDICINE ONLINE 2023年第4期47卷 103245-103245页

作者： Samarasekera, Tanya Willats, Elissa Green, Mark P. Hardy, Tristan Rombauts, Luk Zander-Fox, Deirdre Monash IVF Melbourne Australia Univ Melbourne Fac Sci Sch Biosci Melbourne Australia Monash Hlth Melbourne Australia Monash Univ Biomed Discovery Inst Fac Biomed Sci Melbourne Australia Univ Adelaide Fac Hlth & Med Sci Sch Biomed Adelaide Australia

Research question: Does advanced paternal age (APA;>= 40 years) contribute to a higher incidence of paternal origin aneuploidy in preimplantation embryos? Design: This was a multicentre retrospective study of single-nucleotide polymorphism (snp) microarray (Natera and Karyomapping) preimplantation genetic testing (PGT) outcomes of blastocyst-stage embryos. Whole-chromosome aneuploidy analysis was performed on 2409 embryos from 389 male patients undertaking 681 assisted reproductive technology (ART) cycles between 2012-2021. Segmental aneuploidy analysis was performed on 867 embryos from 140 men undertaking 242 ART cycles between 2016-2021. Embryos were grouped based on paternal age at sperm collection: <35, 35-39 and >= 40 years. Paternal and maternal origin aneuploidy rates were compared between groups using chi-squared and/or Fisher's exact tests. Results: There was no significant difference across groups in paternal origin whole-chromosome aneuploidy rate, overall (P=0.7561) or when segregated by type (trisomy and monosomy: P=0.2235 and 0.8156) or complexity (single versus 2, 3 or >= 4 aneuploidies: P=0.9733, 0.7517, 0.669 and 0.1481). Conversely, maternal origin whole-chromosome aneuploidy rate differed across groups (P<0.0001) in alignment with differing mean maternal age (P<0.001). Paternal origin deletions were 2.9-fold higher than maternal origin deletions (P=0.0084), independent of age stratification. No significant difference in paternal origin deletions was observed with APA >= 40 compared with the younger age groups (4.8% versus 2.5% and 2.8%, P=0.5292). Individual chromosome aneuploidy rates were too low to perform statistical comparisons. Conclusions: No significant association was found between APA and the incidence of paternal origin aneuploidy in preimplantation embryos, irrespective of type or complexity. Thus, APA may not be an indication for PGT.

关键词： Advanced paternal age Aneuploidy IVF embryo Preimplantation genetic testing snp microarray

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：