Mapping analysis Mapping analysis softwaresoftware

Dr Dr Ian Carr PhD. MCSD.Ian Carr PhD. MCSD.Leeds Institute of Molecular Leeds Institute of Molecular

MedicineMedicineSt James’s University HospitalSt James’s University Hospital

AutozygosityAutozygosity

But!LA = local (common) ancestorLI = local inheritance

AutozygosityAutozygosity

You only know part of the picture

And

What you don’t know can be more important than what you do knowDA = distant (common) ancestor

DI = distant inheritance

AnalysisAnalysis

New wayNew way Send DNA off with £300 per sampleSend DNA off with £300 per sample Wait three weeksWait three weeks Stare at a million uninformative SNPs Stare at a million uninformative SNPs

worth of data and wonder what to do worth of data and wonder what to do with it!with it!

Old wayOld way Spend 1.5 years mapping a family with Spend 1.5 years mapping a family with

highly informative microsatelliteshighly informative microsatellites Analyse data as you goAnalyse data as you go Hope you find something!Hope you find something!

AutoSNPaAutoSNPa

What is it:What is it: It’s one big database which draws pretty It’s one big database which draws pretty

picturespictures There is no maths, because there is no There is no maths, because there is no

complete knowledge of the systemcomplete knowledge of the system

AssumptionsAssumptions All affecteds are consanguineous and have All affecteds are consanguineous and have

the same mutation and hence a common the same mutation and hence a common haplotypehaplotype

AutoSNPA: Pedigree oneAutoSNPA: Pedigree one

First family First family ResultsResults

135Mb region on 135Mb region on chromosome 4chromosome 4

Out comeOut come To many genes: Move To many genes: Move

on.on.

135Mb

AutoSNPA: Pedigree twoAutoSNPA: Pedigree two

Two families Two families New ResultsNew Results

45Mb Region on 45Mb Region on chromosome 4chromosome 4

Out comeOut come Still to many genes: Still to many genes:

Move onMove on

45Mb

AutoSNPA: Pedigree AutoSNPA: Pedigree threethree Three families Three families

New new ResultsNew new Results 4.5Mb region on 4.5Mb region on

chromosome 4chromosome 4 Out comeOut come

8 genes, one good 8 genes, one good candidate: Sequenced candidate: Sequenced it and published.it and published.

4.5Mb

The problem with The problem with AutoSNPaAutoSNPa

It requires a large family with It requires a large family with multiple affected people who will multiple affected people who will give a DNA sample or a number of give a DNA sample or a number of families with the same founder families with the same founder mutation.mutation.

In reality large families are rare as In reality large families are rare as hens teeth and a each family tends hens teeth and a each family tends to have its own mutation.to have its own mutation.

IBDFinderIBDFinder

What is it:What is it: It’s another big database which draws It’s another big database which draws

pretty picturespretty pictures Again no mathsAgain no maths

AssumptionsAssumptions The affecteds are consanguineous and The affecteds are consanguineous and

most have mutations in the same gene.most have mutations in the same gene.

Disease has social stigma, so no pedigree dataDisease has social stigma, so no pedigree data Most unrelated to each other.Most unrelated to each other. 2 have mutations in a different gene.2 have mutations in a different gene. 2 have an IBD region of one SNP in the data set2 have an IBD region of one SNP in the data set

Molar pregnancies and Molar pregnancies and IBDFinderIBDFinder

Number of patients

homozygous for the region

19p-tel 19q-tel

Milk drinkers and Milk drinkers and IBDfinderIBDfinder

The ability for adults to drink milk is The ability for adults to drink milk is relatively new and there are only a few relatively new and there are only a few genotypes that have the phenotype. genotypes that have the phenotype. Therefore most of us are homozygous Therefore most of us are homozygous for the for the LCTLCT gene on chromosome 2 gene on chromosome 2

Problems with IBDfinderProblems with IBDfinder

DNA from affecteds is not always DNA from affecteds is not always easy to come by.easy to come by.

““SAMPLE” SAMPLE” SShadow hadow AAutozygosity utozygosity MMaaPPping by ping by LLinkage inkage

EExclusionxclusion What is it:What is it:

A program that finds disease genes without A program that finds disease genes without the DNA of an affected patient, only DNA the DNA of an affected patient, only DNA from the parents and siblings of affecteds. from the parents and siblings of affecteds.

Assumptions:Assumptions: An inbreed family is 3 times more likely to An inbreed family is 3 times more likely to

have an unaffected kid than an affected one, have an unaffected kid than an affected one, none of whom will be homozygous for the none of whom will be homozygous for the disease causing allele.disease causing allele.

Meckel-Gruber Meckel-Gruber Syndrome Syndrome

(MKS3)(MKS3)

DNA available from individuals with yellow DNA available from individuals with yellow symbols. symbols. No data from affected individualsNo data from affected individuals

SAMPLE test SAMPLE test data data

SAMPLE excludes most of the genome (~98%) and the remaining regions can be checked using microsatellites.

Problems with SAMPLEProblems with SAMPLE

All the pedigree have to have a All the pedigree have to have a mutation in the same gene.mutation in the same gene.

It works at the level of individual It works at the level of individual SNPs and does not consider SNPs and does not consider extended haplotypes.extended haplotypes.

PhaserPhaser

What is itWhat is it A program that uses logic to determine the A program that uses logic to determine the

phase of the genotypes of the SNPs on each phase of the genotypes of the SNPs on each chromosome. chromosome.

It can then calculate how autozygous each It can then calculate how autozygous each person is, how related a pedigree is to person is, how related a pedigree is to another and to find common haplotypes in another and to find common haplotypes in affecteds. affecteds.

RequirementsRequirements It needs SNP data for parents and at less two It needs SNP data for parents and at less two

children and ideally a number of pedigrees.children and ideally a number of pedigrees.

Meckel-Meckel-Gruber Gruber

Syndrome Syndrome (MKS3)(MKS3)

Phaser identifies segments Phaser identifies segments of chromosomes present of chromosomes present individuals allowing the individuals allowing the user to analysis dominant user to analysis dominant and recessive diseases.and recessive diseases.

Degree of relatednessDegree of relatedness

Degree of relatednessDegree of relatedness

By knowing how related two pedigrees are, it is possible By knowing how related two pedigrees are, it is possible to judge how likely they are to have a common haplotypeto judge how likely they are to have a common haplotype

The problem with PhaserThe problem with Phaser

It has not been tested exhaustively It has not been tested exhaustively and so may not work!and so may not work!

Sequence analysisSequence analysis

Sanger sequencing mutation Sanger sequencing mutation detectiondetection

Next generation clonal sequencing Next generation clonal sequencing mutation detectionmutation detection

GenescreenGenescreen

Rapid Rapid detection and detection and annotation of annotation of sequence sequence variantsvariants

Annotation of simple Annotation of simple mutationsmutations

Single base Single base mutations mutations are are automaticallautomatically annotated y annotated with with genomic, genomic, cDNA and cDNA and protein protein information. information.

Annotation of complex Annotation of complex mutationsmutations

Heterozygous Heterozygous indels are indels are deconvoluted deconvoluted and annotated. and annotated. This window This window also annotates also annotates indels and indels and homozygous homozygous insertions and insertions and deletionsdeletions

Exporting dataExporting data Plain text, LOVD import file or a web page.Plain text, LOVD import file or a web page.

The The webpage webpage is is updatable updatable and so and so acts a data acts a data display display and data and data base.base.

Clonal Clonal sequencingsequencing Nothing lasts for ever so the current sequencing project is Nothing lasts for ever so the current sequencing project is

to create a program that analysers Illumina sequence to create a program that analysers Illumina sequence data.data.

At the moment the base program analyses data at a rate At the moment the base program analyses data at a rate of 3.6 billion bases an hour or 320Mb of data a minute.of 3.6 billion bases an hour or 320Mb of data a minute.

Underlying data for a Underlying data for a heterozygous base changeheterozygous base change

Underlying data for a Underlying data for a heterozygous base pair insertionheterozygous base pair insertion

All released programs can be obtained All released programs can be obtained from: from: www.Autozygosity.comwww.Autozygosity.com