The Mutation Mapping and Developmental Analysis Project (MMDAP; Brigham and Women’s Hospital, Harvard Medical School), has been providing mouse SNP genotyping and genetic mapping services to the mouse community for over three years. We have worked with more than 100 investigators worldwide on over 400 projects mapping monogenic mutants, modifiers, QTL loci and LOH loci, as well as providing colony maintenance genotyping for detecting strain contamination and congenic strain generation. We offer both whole genome genotyping with our 768 SNP panel and custom genotyping.
Whole genome genotyping: 768 SNP panel
MMDAP, together with the Broad Institute of MIT and Harvard Center for Genotyping and Analysis (CGA), offers genotyping of a fixed whole genome panel of 768 mouse SNPs. The 768 panel, which utilizes the Illumina genotyping platform, has an average SNP density of 3 Mb across autosomes and 7 Mb across Chr. X. The panel was designed to optimize polymorphism with C57BL/6J, such that the average number of informative SNPs between C57BL/6J and common inbred strains is 550; however, the panel is suitable for many strain combinations. Support from NIH grants to MMDAP (U01-HD43430; NICHD) and CGA (U54 RR020278-01; NCRR) enables us to offer genotyping of the 768 panel at $68 per sample.
SNPs were obtained from the GNF2 and WTCHG1 public database submissions. The number of informative SNPs in the 768 panel between common inbred strains is shown below. Lists of informative SNPs between strain combinations (including strains not shown), chromosome, Mb position and sequence are available upon request.
|
|
C57BL/ 6J
|
129X1/ SvJ
|
BALB/cJ
|
C3H/HeJ
|
DBA/2J
|
FVB/NJ
|
A/J
|
CBA/J
|
C57BL/ 10J
|
|
C57BL/6J
|
|
508
|
497
|
598
|
555
|
539
|
581
|
562
|
68
|
|
129X1/SvJ
|
|
|
315
|
333
|
365
|
316
|
367
|
313
|
455
|
|
BALB/cJ
|
|
|
|
233
|
323
|
285
|
203
|
262
|
448
|
|
C3H/HeJ
|
|
|
|
|
241
|
294
|
226
|
111
|
552
|
|
DBA/2J
|
|
|
|
|
|
323
|
325
|
235
|
518
|
|
FVB/NJ
|
|
|
|
|
|
|
274
|
281
|
492
|
|
A/J
|
|
|
|
|
|
|
|
276
|
547
|
|
CBA/J
|
|
|
|
|
|
|
|
|
514
|
|
C57BL/10J
|
|
|
|
|
|
|
|
|
|
Custom SNP Genotyping
MMDAP, together with the Harvard Partners Center for Genetics and Genomics, offers custom SNP panel design and genotyping with the Sequenom iPLEX Gold platform. iPLEX Gold chemistry allows for plexing of up to 40 SNPs per reaction (plex). Custom panels are ideally suited for chromosome- or region-specific fine mapping.
Costs for Custom SNP Genotyping: Each custom project has 2 charges: a one-time fixed set-up/design charge and a genotyping charge which depends on the number of samples and reactions genotyped per submission.
Set-up/design fee: $22 per SNP assay
Genotyping fee: $4.27 per well plus chip charge (# wells = # samples x # plexes)
Sample billing costs:
|
Samples
|
Number of plexes/reactions
|
Chip charge
|
Total genotyping cost
|
|
1 plex
|
2 plexes
|
3 plexes
|
1 plex
|
2 plexes
|
3 plexes
|
1 plex
|
2 plexes
|
3 plexes
|
|
up to 40 SNPs
|
up to 80 SNPs
|
up to 120 SNPs
|
up to 40 SNPs
|
up to 80 SNPs
|
up to 120 SNPs
|
up to 40 SNPs
|
up to 80 SNPs
|
up to 120 SNPs
|
|
50
|
$213.50
|
$427.00
|
$640.50
|
$184.00
|
$184.00
|
$184.00
|
$397.50
|
$611.00
|
$824.50
|
|
96
|
$409.92
|
$819.84
|
$1,229.76
|
$184.00
|
$184.00
|
$184.00
|
$593.92
|
$1,003.84
|
$1,413.76
|
|
192
|
$819.84
|
$1,639.68
|
$2,459.52
|
$184.00
|
$184.00
|
$368.00
|
$1,003.84
|
$1,823.68
|
$2,827.52
|
|
384
|
$1,639.68
|
$3,279.36
|
$4,919.04
|
$184.00
|
$368.00
|
$552.00
|
$1,823.68
|
$3,647.36
|
$5,471.04
|
|
