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Prenatal microarray comparative genomic hybridization: Experience from the two first years of activity at the Lyon university-hospital

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JOURNAL OF GYNECOLOGY OBSTETRICS AND HUMAN REPRODUCTION 2017年第3期46卷 275-283页

作者： Pons, L. Till, M. Alix, E. Abel, C. Boggio, D. Bordes, A. Caloone, J. Raskin, F. C. Chatron, N. Cordier, M. -P. Fichez, A. Labalme, A. Lajeunesse, C. Liaras, E. Massoud, M. Miribel, J. Agnon, E. Schluth-Bolard, C. Vichier-Cerf, A. Edery, P. Attia, J. Huissoud, C. Rudigoz, R. C. Massardier, J. Gaucherand, P. Sanlaville, D. HCL Grp Hosp Est Serv Genet 59 Blvd Pinel F-69677 Bron France Univ Claude Bernard Lyon 1 F-69008 Lyon France HCL Grp Hosp Est Dept Obstet & Gynecol F-69500 Bron France HCL Ctr Hosp Croix Rousse Dept Obstet & Gynecol F-69004 Lyon France HCL Ctr Hosp Lyon Sud Dept Obstet & Gynecol F-69310 Pierre Benite France Ctr Rech Neurosci Lyon INSERM U1028 CNRS UMR 5292 Equipe Gendev F-69500 Bron France

Objectives. - This study aims to describe how microarray comparative genomic hybridization (aCGH) has shifted to become a prenatal diagnosis tool at the Lyon university-hospital. Materials and methods. - This retrospective study included all patients who were referred in the 3 pluridisciplinary centers for prenatal diagnosis of the Lyon university-hospital and who received a prenatal aCGH between June 2013 and June 2015. aCGH was systematically performed in parallel with a karyotype, using the PreCytoNEM array design. Results. - A total of 260 microarrays were performed for the following indications: 249 abnormal ultrasounds (95.8%), 7 characterizations of chromosomal rearrangements (2.7%), and 4 twins with no abnormal ultrasounds (1.5%). With a resolution of 1 mega base, we found 235 normal results (90.4%), 23 abnormal results (8.8%) and 2 non-returns (0.8%). For the chromosomal rearrangements visible on the karyotype, aCGH identified all of the 12 unbalanced rearrangements and did not identify the 2 balanced rearrangements. Among the fetuses with normal karyotypes, 11 showed abnormal microarray results, corresponding to unbalanced cryptic chromosomal rearrangements (4.2%). Conclusion. - Transferring aCGH to a prenatal diagnosis at the Lyon university-hospital has increased the detection rate of chromosomal abnormalities by 4.2% compared to the single karyotype. (C) 2017 Elsevier Masson SAS. All rights reserved.

关键词： Prenatal diagnosis microarray comparative genomic hybridization Abnormal ultrasounds Characterization of chromosomal rearrangements

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Chromosomal microarray Analysis Using Array comparative genomic hybridization on DNA from Amniotic Fluid and Chorionic Villus Sampling

Chromosomal Microarray Analysis Using Array Comparative Geno...

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作者： Ankita Patel

Chromosomal microarray analysis offers an objective high resolution view of copy number changes in the genome that contribute to genomic disorders in various clinical setting such as postnatal, prenatal, and oncology. Here, we describe a fast and reliable method of using chromosomal microarray analysis in detection of genomic imbalances that may be associated with congenital malformations in a prenatal setting. Results can be obtained in 4–5 days using direct amniotic fluid (AF) or chorionic villus samples (CVS). less

关键词： microarray comparative genomic hybridization microarray comparative genomic hybridization DNA Extraction Cell Lysis Protein Precipitation Fluorescence Labeling Enzyme Digestion Homo sapiens Prenatal diagnosis

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Comprehensive Genetic Analysis of Non-syndromic Autism Spectrum Disorder in Clinical Settings

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JOURNAL OF AUTISM AND DEVELOPMENTAL DISORDERS 2021年第12期51卷 4655-4662页

作者： Ohashi, Kei Fukuhara, Satomi Miyachi, Taishi Asai, Tomoko Imaeda, Masayuki Goto, Masahide Kurokawa, Yoshie Anzai, Tatsuya Tsurusaki, Yoshinori Miyake, Noriko Matsumoto, Naomichi Yamagata, Takanori Saitoh, Shinji Nagoya City Univ Dept Pediat & Neonatol Grad Sch Med Sci Nagoya Aichi Japan Jichi Med Univ Dept Pediat Shimotsuke Tochigi Japan Yokohama City Univ Dept Human Genet Grad Sch Med Yokohama Kanagawa Japan Sagami Womens Univ Fac Nutr Sci Sagamihara Kanagawa Japan

Although genetic factors are involved in the etiology of autism spectrum disorder (ASD), the significance of genetic analysis in clinical settings is unclear. Forty-nine subjects diagnosed with non-syndromic ASD were analyzed by microarray comparative genomic hybridization (CGH) analysis, whole-exome sequencing (WES) analysis, and panel sequencing analysis for 52 common causative genes of ASD to detect inherited rare variants. Genetic analysis by microarray CGH and WES analyses showed conclusive results in about 10% of patients, however, many inherited variants detected by panel sequencing analysis were difficult to interpret and apply in clinical practice in the majority of patients. Further improvement of interpretation of many variants detected would be necessary for combined genetic tests to be used in clinical settings.

关键词： Autism spectrum disorder Genetic analysis Whole-exome sequencing microarray comparative genomic hybridization

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Myelodysplastic syndromes in a pediatric patient with Cri du Chat syndrome with a ring chromosome 5

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INTERNATIONAL JOURNAL OF HEMATOLOGY 2020年第5期112卷 728-733页

作者： Nozawa, Akifumi Ozeki, Michio Yasue, Shiho Endo, Saori Kadowaki, Tomonori Ohnishi, Hidenori Muramatsu, Hideki Hama, Asahito Takahashi, Yoshiyuki Kojima, Seiji Fukao, Toshiyuki Gifu Univ Grad Sch Med Dept Pediat 1-1 Yanagido Gifu 5011194 Japan Natl Hosp Org Nagara Med Ctr Dept Pediat Gifu 5028558 Japan Nagoya Univ Grad Sch Med Dept Pediat Showa Ku Nagoya Aichi 4668650 Japan Japanese Red Cross Nagoya First Hosp Childrens Med Ctr Dept Hematol & Oncol Nakamura Ku Nagoya Aichi 4538511 Japan

Few hematological complications have previously been reported in association with Cri du Chat syndrome (CdCS). A case of myelodysplastic syndromes (MDS) in a pediatric patient with CdCS is herein presented. A 17-year-old female with CdCS caused by ring chromosome 5 was admitted to the hospital for investigation of a 1-month history of anemia. Based on the morphological findings of bone marrow, the patient was diagnosed with refractory cytopenia with multilineage dysplasia. The risk group was classified as intermediate-1 in the International Prognostic Scoring System (IPSS), and low in the revised IPSS. Assessment by microarray comparative genomic hybridization (CGH) identified the breakpoints of ring chromosome 5 as 46,XX,r(5)(p14.3q35.3). This revealed that the 5q terminal deletion did not include the common deleted region of MDS with del(5q). Treatment with azacitidine was initiated to control disease progression and improve quality of life. At baseline, the patient had a mean transfusion requirement of 3 units/month, which decreased to 2 units/month after six cycles of azacitidine and to 1 unit/month after 10 cycles of azacitidine. Cytopenia observed in the presented case seemed irrelevant to ring chromosome 5 which is the causative cytogenetic abnormality of CdCS, and further analyses may be needed to clarify the pathogenesis.

关键词： Pediatric hematology Neurofibromatosis type 1 Ring chromosome 5 microarray comparative genomic hybridization Heterozygous missense mutation

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An efficient genetic test flow for multiple congenital anomalies and intellectual disability

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PEDIATRICS INTERNATIONAL 2020年第5期62卷 556-561页

作者： Yokoi, Takayuki Enomoto, Yumi Tsurusaki, Yoshinori Harada, Noriaki Saito, Toshiyuki Nagai, Jun-ichi Naruto, Takuya Kurosawa, Kenji Kanagawa Childrens Med Ctr Div Med Genet Yokohama Kanagawa Japan Kanagawa Childrens Med Ctr Clin Res Inst Yokohama Kanagawa Japan Kanagawa Childrens Med Ctr Dept Clin Lab Yokohama Kanagawa Japan Jikei Univ Dept Pediat Sch Med Tokyo Japan Tokyo Med & Dent Univ Grad Sch Dept Pediat & Dev Biol Grad Sch Tokyo Japan

Background Genetic testing has enabled the diagnosis of multiple congenital anomalies and/or intellectual disabilities. However, because of the phenotypic variability in these disorders, selection of an appropriate genetic test can be difficult and complex. For clinical examination, particularly in clinical facilities, a simple and standardized system is needed. Methods We compared microarray comparative genomic hybridization and clinical exome sequencing with regard to diagnostic yield, cost, and time required to reach a definitive diagnosis. After first performing G-banding for 200 patients with multiple congenital anomalies and/or intellectual disability, as a subsequent genetic test, microarray and clinical exome sequencing were compared with regard to diagnostic yield, cost, and time required. Results There was no obvious difference in the diagnostic rate between the two methods;however, clinical exome sequencing was superior in terms of cost and time. In addition, clinical exome sequencing could sufficiently identify copy number variants, and even smaller copy number variants could be identified. Conclusions Clinical exome sequencing should be implemented earlier as a genetic test for undiagnosed patients with multiple congenital anomalies and/or intellectual disabilities. Our results can be used to establish inspection methods in clinical facilities.

关键词： clinical exome sequencing copy number variant intellectual disability microarray comparative genomic hybridization multiple congenital anomaly

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Exome Sequencing

Exome Sequencing

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作者： Aruna Pal

Exome sequencing, also known as whole exome sequencing (WES or WXS), is a technique for sequencing all the expressed genes in a genome (known as the exome). It has a major advantage over whole genome sequencing since exon or coding region is very less 1–2% of total genome, hence very less sequencing is required and it saves cost, time, and effort of scientists. Outline of the protocol for exome sequencing involves the following steps: DNA samples should be fragmented and biotinylated, oligonucleotide probes (baits) are to be used to selectively hybridize to target regions in the genome. Magnetic streptavidin beads are used to bind to the biotinylated probes. The nontargeted portion of the genome is to be washed away, and the polymerase chain reaction (PCR) is used to amplify the sample, enriching the sample for DNA from the target region. The sample should be sequenced before proceeding to bioinformatic analysis. Array-based methods are similar except that the probes are bound to a high-density microarray. Some commonly employed exome kits were described. A brief idea for data analysis pertaining to exome sequencing has been depicted. Protocol was described with practical examples of case studies. less

关键词： Whole-exome sequencing Whole-genome Sequencing PCR microarray DNA Sequencing microarray comparative genomic hybridization Deep Sequencing Multiplex PCR Statistical Calculation Variant Calling Western Blot Data analysis Exome Hybrid capture Molecular inversion probe Biotinylated probes Exome kit Magnetic streptavidin beads

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A 235 Kb deletion at 17q21.33 encompassing the COL1A1, and two additional secondary copy number variants in an infant with type I osteogenesis imperfecta: A rare case report

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MOLECULAR GENETICS & genomic MEDICINE 2020年第6期8卷 e1241页

作者： Numbere, Numbereye Weber, David R. Porter, George, Jr. Iqbal, Mohammed A. Univ Rochester Med Ctr Dept Pathol & Lab Med 601 Elmwood Ave Rochester NY 14642 USA Univ Rochester Med Ctr Dept Pediat Pediat Endocrinol Rochester NY 14642 USA Univ Rochester Med Ctr Dept Pediat Pediat Cardiol Rochester NY 14642 USA

Background Osteogenesis imperfecta (OI) is a rare group of disorders characterized by increased susceptibility to fractures due to genetically determined bone fragility. About 90% of cases are due to mutations in COL1A1 (17q21.33) or COL1A2 (7q21.3) resulting in quantitative or qualitative defects in type I collagen, a key structural constituent of bone. OI due to complete COL1A1 deletion is rare. Methods We present a case of OI type I in a Caucasian female referred at 10 months of age for investigation of multiple fractures associated with minimal or no known trauma, small stature, and blue sclera. Her father has four to five lifetime fractures, blue sclera, normal stature, and a 14.5 kilobase (kb) deletion of COL1A1 detected by targeted array performed at an outside institution. microarray comparative genomic hybridization was performed on the proband and all members of the family. Results A previously unreported 235 kb deletion at 17q21.33 encompassing COL1A1, ITGA3, PDK2, SGCA, and HILS1 was detected in the proband. Also identified in both the proband and sibling is a maternally inherited 283 kb gain at 8p21.3 encompassing CSGALNACT1 and a 163 kb loss at 10q21.3 encompassing CTNNA3. Analysis in the father revealed the same size deletion at 17q21.33 as in the proband. Conclusion Together with previously reported cases of COL1A1 deletions, this case report emphasizes the importance of a whole-genome DNA copy number assessment in patients suspected for OI, which will elucidate the presence of precise COL1A1 deletions and any pathogenic secondary copy number variations.

关键词： aCGH MACGH microarray comparative genomic hybridization osteogenesis imperfecta

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Whole-Genome Capture of Ancient DNA Using Homemade Baits

Whole-Genome Capture of Ancient DNA Using Homemade Baits

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作者： Gloria González Fortes Johanna L. Paijmans

For many archaeological and paleontological samples, the relative content of endogenous compared to contaminant DNA is low. In such cases, enriching sequencing libraries for endogenous DNA, prior to sequencing can make the final research project more cost-effective. Here, we present an in-solution enrichment protocol based on homemade baits that can be applied to recover complete nuclear genomes from ancient remains. The approach is based on the preparation of DNA baits by biotinylated adapter ligation. The procedure has been developed for use with human remains but can be adapted to other species or target regions by choosing the appropriate template DNA from which to build the capture baits. By using homemade rather than commercially acquired baits, this protocol may offer increased flexibility and cost efficiency. less

关键词： Sonication Real-time PCR microarray comparative genomic hybridization ChIP-on-chip HPLC DNA Ligation Homo sapiens Ancient DNA Whole-genome target enrichment Homemade capture baits hybridization capture

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comparative genomic hybridization (CGH) in Genotoxicology

Comparative Genomic Hybridization (CGH) in Genotoxicology

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作者： Adi Baumgartner Veronika Hartleb Jim D. Taylor

In the past two decades, comparative genomic hybridization (CGH) and array CGH have become indispensable tools in clinical diagnostics and toxicological risk assessment. Initially developed for the genome-wide screening of chromosomal imbalances, that is, copy-number variations in tumor cells, both CGH and array CGH have been employed in genotoxicology and most recently in toxicogenomics. The latter allows a multi-end point analysis of how particular genes react to toxic agents, revealing changes in signaling pathways and other underlying molecular mechanisms. This chapter provides background on the use of CGH and array CGH in the context of genotoxicology, and also a protocol for conventional CGH, so that the basic principles of this methodology can be better understood. Conventional and array CGH investigate DNA expression patterns, copy-number variations across the whole genome, and loss of heterozygosity after genotoxic damage. Array CGH is still cost-intensive but produces exponentially more data, requiring suitable analytical algorithms and sophisticated bioinformatic analysis. As toxicogenomics is an emerging sub-discipline of toxicology research, effectively evaluating toxicogenomic microarray data can be hugely advantageous for human risk assessment, even though international regulatory guidelines on toxicogenomics have yet to be fully agreed and implemented. less

关键词： comparative genomic hybridization microarray comparative genomic hybridization microarray PCR Agarose Gel Electrophoresis In Situ hybridization Titration CGH Toxicogenomics genomic imbalances Genotoxicology

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Detection of Aneuploidy and Unbalanced Rearrangements Using comparative genomic hybridization microarrays

Detection of Aneuploidy and Unbalanced Rearrangements Using ...

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作者： Lorena Rodrigo Vivó Carmen Rubio Lluesa

comparative genomic hybridization arrays (aCGH) allow the analysis of all 24 chromosome aneuploidies and chromosome rearrangements in the same single (or few) biopsied cells in a short period (less than 24 h). When applied to preimplantation genetic diagnosis (PGD) and screening (PGS) this technique can improve the selection of embryos for transfer and therefore also the reproductive outcomes. In this chapter, we describe the CGH microarray protocol for PGS and PGD used in our laboratory. less

关键词： microarray comparative genomic hybridization Genome Amplification Rearrangement comparative genomic hybridization microarray Biopsy PCR Cell Lysis DNA Extraction Agarose Gel Electrophoresis Data analysis Homo sapiens Aneuploidy Preimplantation genetic diagnosis (PGD) Preimplantation genetic screening (PGS)

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