New developments in high-throughput resequencing and variation detection using high density microarrays

Warrington, Janet A.; Shah, Nila; Chen, Xiyin; Janis, Michael; Liu, Chunmei; Kondapalli, Sangeetha; Reyes, Vivian; Savage, Michael P.; Zhang, Zhaomei; Watts, Richard A.; deGuzman, Maria Krishna; Berno, Anthony; Snyder, Jim; Baid, Jyoti

doi:10.1002/humu.10075

Cited by 66 publications

(37 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…2,3 We used this method to develop a comprehensive high-throughput resequencing system focusing on ALS as well as other neurodegenerative diseases.…”

Section: Ith Recent Progressmentioning

confidence: 99%

Development of a High-Throughput Microarray-Based Resequencing System for Neurological Disorders and Its Application to Molecular Genetics of Amyotrophic Lateral Sclerosis

Takahashi¹,

Seki²,

Ishiura³

et al. 2008

Arch Neurol

View full text Add to dashboard Cite

Background: Comprehensive resequencing of the causative and disease-related genes of neurodegenerative diseases is expected to enable (1) comprehensive mutational analysis of familial cases, (2) identification of sporadic cases with de novo or low-penetrant mutations, (3) identification of rare variants conferring disease susceptibility, and ultimately (4) better understanding of the molecular basis of these diseases.Objective: To develop a microarray-based highthroughput resequencing system for the causative and disease-related genes of amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases.Design: Validation of the system was conducted in terms of the signal-to-noise ratio, accuracy, and throughput. Comprehensive gene analysis was applied for patients with ALS.Subjects: Ten patients with familial ALS, 35 patients with sporadic ALS, and 238 controls. Results:The system detected point mutations with 100% accuracy and completed the resequencing of 270 kilobase pairs in 3 working days with greater than 99.9% accuracy of base calls, or the determination of base(s) at each position. Analysis of patients with familial ALS revealed 2 SOD1 mutations. Analysis of the 35 patients with sporadic ALS revealed a previously known SOD1 mutation, S134N, a novel putative pathogenic DCTN1 mutation, R997W, and 9 novel variants including 4 nonsynonymous heterozygous variants consisting of 2 in ALS2, 1 in ANG, and 1 in VEGF that were not found in the controls. Conclusion:The DNA microarray-based resequencing system is a powerful tool for high-throughput comprehensive analysis of causative and disease-related genes. It can be used to detect mutations in familial and sporadic cases and to identify numerous novel variants potentially associated with genetic risks.

show abstract

“…2,3 We used this method to develop a comprehensive high-throughput resequencing system focusing on ALS as well as other neurodegenerative diseases.…”

Section: Ith Recent Progressmentioning

confidence: 99%

Development of a High-Throughput Microarray-Based Resequencing System for Neurological Disorders and Its Application to Molecular Genetics of Amyotrophic Lateral Sclerosis

Takahashi¹,

Seki²,

Ishiura³

et al. 2008

Arch Neurol

View full text Add to dashboard Cite

show abstract

“…14,15 Briefly, specific PCR was conducted for each exon using previously reported primers. 6 After quantification of the PCR products, they were pooled equimolarly, fragmented with DNase I, labeled with biotin, hybridized to microarrays, stained with streptoavidin-phycoerythrin, washed and scanned.…”

Section: Mutational Analysismentioning

confidence: 99%

Comprehensive mutational analysis of LRRK2 reveals variants supporting association with autosomal dominant Parkinson's disease

et al. 2011

View full text Add to dashboard Cite

“…Neben der Untersuchung der Genexpression wird die Array-Technologie auch verwendet, um die jetzt bekannte Sequenzinformation über ein humanes Genom abzubilden und durch Hybridisierung mit genomischer DNA einzelner Individuen systematisch nach genomischen Polymorphismen und Mutationen zu untersuchen (63). Damit wird erwartet, dass Polymorphismen in regulatorischen und nicht Protein kodierenden Bereichen identifiziert werden können, die bedeutsam für Fehlregulationen in der Zytokinkaskade (6), der Matrixbildung (37, 38) oder der Immunantwort (40) bei Gelenkerkrankungen sein können.…”

Section: N Dna-arraysunclassified

Neue Aspekte der molekularbiologischen Diagnostik Array-Technologie und Expressionsprofile für die Charakterisierung rheumatischer Erkrankungen

Häupl¹,

Burmester

Stuhlmüller

2002

Z Rheumatol

View full text Add to dashboard Cite

Increasing availability of high throughput technologies, exponentially growing information about the human genome and gene expression, and the growing global network of databases on systematic biomedical information will change our view on inflammatory rheumatic diseases in a revolutionary way. Several research laboratories have already generated initial extensive datasets on gene expression analysis. Application of this technique has demonstrated that in addition to a precise analysis, verification and validation of the results also on the level of cell populations, a meticulous characterization of the patients according to current conventional clinical, laboratory, imaging and histological standards is essential. For functional interpretation, in vitro tests, animal models and therapeutic studies will provide further information. Bioinformatic structuring and development is needed for the large amounts of data. After an initial genome-wide screening, the objective is to identify those genes, which will allow characterization of the disease, classification according to molecular pathophysiology, evaluation of the prognosis and prediction of the correct and most potent therapeutic regimen. Derived from the improved knowledge about the molecular mechanisms, new and--as to expect--the crucial approaches for an effective therapy against chronic inflammation, organ destruction and pathological immune response in rheumatic diseases will emerge.

show abstract

New developments in high-throughput resequencing and variation detection using high density microarrays

Cited by 66 publications

References 8 publications

Development of a High-Throughput Microarray-Based Resequencing System for Neurological Disorders and Its Application to Molecular Genetics of Amyotrophic Lateral Sclerosis

Development of a High-Throughput Microarray-Based Resequencing System for Neurological Disorders and Its Application to Molecular Genetics of Amyotrophic Lateral Sclerosis

Comprehensive mutational analysis of LRRK2 reveals variants supporting association with autosomal dominant Parkinson's disease

Neue Aspekte der molekularbiologischen Diagnostik Array-Technologie und Expressionsprofile für die Charakterisierung rheumatischer Erkrankungen

Contact Info

Product

Resources

About