SNP을 대량으로 typing 하기 위한 Biochip http://en.wikipedia.org/wiki/SNP_array GWAS 연구 등에 활용된다.

이 실험결과를 관리하는 정보관리기술

• SNPFile
• SNPpy
• Shellfish
• Using R

4배체(tetraploid) 데이터 관련 프로그램

• ClusterCall: 4배체 genotype calling

데이터베이스 만들기 #

SNP array 데이터베이스를 만드는데 중간에 막힘. 대안은?

1. HDF5를 쓰면 충분할 것이라고 생각했는데, 저장상태(append) 검색기능을 쓰기 위해서는 HDF5가 777k 만큼의 컬럼수를 허용하지 않는다. 그 기능을 안쓰면 저장하는데 넘 오래 걸림. 'AA'를 0으로 바꾸는 작업도 매우 오래 걸림.
2. Relational database도 고려해봤으나, 컬럼수가 최대 만개가 넘지 아니함.

--Hyungyong Kim, 2013-10-25

관련정보 #

• Evaluation of copy number variation detection for a SNP array platform. BMC Bioinformatics 2014-02-21: CNV 탐지에 있어 PennCNV가 현저히 우수함
• Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform. BMC Bioinformatics 2011-05-31: CNV 탐지 프로그램 비교
• database backed program for management of SNP data?

Incoming Links #

[Medical Scholarly Articles] About (MedicalScholarlyArticle 0) #

• A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies

[Codes] About (Code 1) #

• GISTIC
• PennCNV
• adegenet

Related Datasets (Dataset 2) #

• 한국인칩

Related Software Applications (SoftwareApplication 3) #

• ASreml
• KING

[Software Applications] About (SoftwareApplication 4) #

• GenomeStudio

Related Products (Product 5) #

• CanineHD Whole-Genome Genotyping BeadChip
• EquineSNP50 BeadChip
• Genome-Wide Human SNP Array 6.0

Related Articles (Article 6) #

• Biochip
• CNV calling from NGS data
• Copy-number variation
• Dog
• Opportunities and challenges of whole-genome and -exome sequencing
• QTL
• Selective sweep
• 암 맞춤의학과 생물정보학

Related Education Events (EducationEvent 7) #

• Genomics and Precision Medicine

Related Medical Conditions (MedicalCondition 8) #

• Prostate cancer

Related Medical Scholarly Articles (MedicalScholarlyArticle 9) #

• Complex disease and phenotype mapping in the domestic dog
• CODEX: a normalization and copy number variation detection method for whole exome sequencing
• Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data
• Methods of integrating data to uncover genotype–phenotype interactions
• SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data
• The landscape of somatic copy-number alteration across human cancers

Related Codes (Code 10) #

• ASCAT
• Bioconductor
• ClusterCall
• saasCNV

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