Genetic mapping

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
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

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 = 0.0025)

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