Physical and transcript mapping Physical mapping Transcript identification

Physical and transcript mapping Somatic Cell Hybrids –Monochromosomal –Polychromosomal –Radiation hybrids

Physical and transcript mapping Somatic Cell Hybrids –Subchromosomal assignment by PCR of hybrids with different chromosomal content.

Physical and transcript mapping Radiation hybrid maps –Random breakpoints. –Ordering of markers.

Physical and transcript mapping Fluorescence in situ hybridization –YAC hybridization. –Translocation breakpoint 3q26 and 17q23.

Physical and transcript mapping Fluorescence in situ hybridization –Chromosome painting. –Chromosome 8 paint.

Physical and transcript mapping Flow sorting chromosomes –Fluorescent dye labeled chromosomes. –Flow karyogram. –Fractionate whole chromosomes Yeast/YACs

Physical and transcript mapping Pulsed field electrophoresis –Rotating magnetic field. –Large DNA fragments.

Physical and transcript mapping Clone contig –Overlapping DNA fragments.

Physical and transcript mapping Chromosome walking –Clone to clone hybridization.

Physical and transcript mapping Inverse PCR –Clone flanking unique DNA sequences.

Physical and transcript mapping Bubble PCR –Amplification of uncharacterized sequences flanking known DNA.

Physical and transcript mapping PCR based screening –Amplification of row, column and plate pools for clone identification.

Physical and transcript mapping Contig assembly –YAC contig assembly by STS content mapping.

Physical and transcript mapping Inter-SINE PCR –Amplify unique sequences between repeats. –Species specific (Alu in primates).

Physical and transcript mapping Zoo blot –Study highly conserved sequences. –Species specific.

Physical and transcript mapping Exon trapping

Physical and transcript mapping cDNA selection using magnetic bead capture

Genetic mapping Genetic markers Recombinants Genetic vs. Physical distances

Genetic mapping MarkerNumberFeatures RFLPs>10 5 diallelic max het 0.5 VNTRs mini>10 4 many alleles high het VNTRsmic>10 5 many alleles high het SNPs>10 6 less informative than VNTRs

Genetic mapping Defining recombinants

Genetic mapping Single vs. Double recombinants

Genetic mapping Relationship between genetic and physical maps for human chromosome 19

Genetic mapping Recognizing recombinants AD disorder A)III-6 is recombinant (disorder + A2 allele) B)III-1 –III-5 are non recomb and III-6 recomb or III-1 – II-5 are recomb and III-6 is non- recomb C)III-7 and III-8 have disorder but the A1 allele may not be identical by descent

Genetic mapping LOD score ratio of likelihood linked recombination fraction = theta)/not linked (recombination fraction = 0.5) Positive in favor of linkage (+3) Negative scores against linkage (-2) Curve 1 linkage (Z>3) no recombinants Curve 2 linkage (Z>3) recombination fraction 0.23 Curve 3 no linkage (Z<-2) for recombination fractions below 0.12 Curve 4 inconclusive

Genetic mapping Multipoint mapping Highest peaks are most likely locations Odds in favor of a position are measured by the degree to which the highest peak overtops its rivals LOD scores dip near markers that show recombinants with the disease

Genetic mapping Double recombinants suggest errors Probability of a true double recombinant with markers 5cM apart is small (below 0.05 x 0.05 = )

Genetic mapping Autozygosity mapping Mapping for markers that are identical by descent Congenital deafness Affected members all homozygous for AFMa052yb5 and D2S158 Gene between AFMb346ye5 and D2S174