1. Physical and transcript mapping
Physical mapping
Transcript identification

2. Physical and transcript mapping
Somatic Cell Hybrids
Monochromosomal
Polychromosomal
Radiation hybrids

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

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

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

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

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

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

19. Physical and transcript mapping
Clone contig
Overlapping DNA fragments.

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

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

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

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

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

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

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

35. Physical and transcript mapping
Exon trapping

37. Physical and transcript mapping
cDNA selection using magnetic bead capture

39. Genetic mapping Genetic markers Recombinants
Genetic vs. Physical distances

40. Genetic mapping Marker Number Features
RFLPs >105 diallelic max het 0.5
VNTRs mini >104 many alleles high het
VNTRs mic >105 many alleles high het
SNPs >106 less informative than VNTRs

41. Genetic mapping
Defining recombinants

43. Genetic mapping
Single vs. Double recombinants

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

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

49. 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

51. 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

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

55. 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