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Mapping analysis software Dr Ian Carr PhD. MCSD. Leeds Institute of Molecular Medicine St James’s University Hospital. Autozygosity. LA = local (common) ancestor LI = local inheritance. But!. Autozygosity. You only know part of the picture And
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Mapping analysis softwareDr Ian Carr PhD. MCSD.Leeds Institute of Molecular MedicineSt James’s University Hospital
Autozygosity LA = local (common) ancestor LI = local inheritance But!
Autozygosity You only know part of the picture And What you don’t know can be more important than what you do know DA = distant (common) ancestor DI = distant inheritance
Analysis • Old way • Spend 1.5 years mapping a family with highly informative microsatellites • Analyse data as you go • Hope you find something! • New way • Send DNA off with £300 per sample • Wait three weeks • Stare at a million uninformative SNPs worth of data and wonder what to do with it!
AutoSNPa • What is it: • It’s one big database which draws pretty pictures • There is no maths, because there is no complete knowledge of the system • Assumptions • All affecteds are consanguineous and have the same mutation and hence a common haplotype
AutoSNPA: Pedigree one • First family • Results • 135Mb region on chromosome 4 • Out come • To many genes: Move on. 135Mb
AutoSNPA: Pedigree two • Two families • New Results • 45Mb Region on chromosome 4 • Out come • Still to many genes: Move on 45Mb
AutoSNPA: Pedigree three • Three families • New new Results • 4.5Mb region on chromosome 4 • Out come • 8 genes, one good candidate: Sequenced it and published. 4.5Mb
The problem with AutoSNPa • It requires a large family with multiple affected people who will give a DNA sample or a number of families with the same founder mutation. • In reality large families are rare as hens teeth and a each family tends to have its own mutation.
IBDFinder • What is it: • It’s another big database which draws pretty pictures • Again no maths • Assumptions • The affecteds are consanguineous and most have mutations in the same gene.
Molar pregnancies and IBDFinder Number of patients homozygous for the region 19p-tel 19q-tel • Disease has social stigma, so no pedigree data • Most unrelated to each other. • 2 have mutations in a different gene. • 2 have an IBD region of one SNP in the data set
Milk drinkers and IBDfinder • The ability for adults to drink milk is relatively new and there are only a few genotypes that have the phenotype. Therefore most of us are homozygous for the LCT gene on chromosome 2
Problems with IBDfinder • DNA from affecteds is not always easy to come by.
“SAMPLE” Shadow Autozygosity MaPping by Linkage Exclusion • What is it: • A program that finds disease genes without the DNA of an affected patient, only DNA from the parents and siblings of affecteds. • Assumptions: • An inbreed family is 3 times more likely to have an unaffected kid than an affected one, none of whom will be homozygous for the disease causing allele.
Meckel-Gruber Syndrome (MKS3) • DNA available from individuals with yellow symbols. No data from affected individuals
SAMPLE test data SAMPLE excludes most of the genome (~98%) and the remaining regions can be checked using microsatellites.
Problems with SAMPLE • All the pedigree have to have a mutation in the same gene. • It works at the level of individual SNPs and does not consider extended haplotypes.
Phaser • What is it • A program that uses logic to determine the phase of the genotypes of the SNPs on each chromosome. • It can then calculate how autozygous each person is, how related a pedigree is to another and to find common haplotypes in affecteds. • Requirements • It needs SNP data for parents and at less two children and ideally a number of pedigrees.
Meckel-Gruber Syndrome (MKS3) • Phaser identifies segments of chromosomes present individuals allowing the user to analysis dominant and recessive diseases.
Degree of relatedness • By knowing how related two pedigrees are, it is possible to judge how likely they are to have a common haplotype
The problem with Phaser • It has not been tested exhaustively and so may not work!
Sequence analysis • Sanger sequencing mutation detection • Next generation clonal sequencing mutation detection
Genescreen • Rapid detection and annotation of sequence variants
Annotation of simple mutations • Single base mutations are automatically annotated with genomic, cDNA and protein information.
Annotation of complex mutations • Heterozygous indels are deconvoluted and annotated. This window also annotates indels and homozygous insertions and deletions
Exporting data • Plain text, LOVD import file or a web page. • The webpage is updatable and so acts a data display and data base.
Clonal sequencing • Nothing lasts for ever so the current sequencing project is to create a program that analysers Illumina sequence data. • At the moment the base program analyses data at a rate of 3.6 billion bases an hour or 320Mb of data a minute.
All released programs can be obtained from: www.Autozygosity.com