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Mammalian Genotyping Service

Genetic Research

 

Screening Sets

Screening Sets Marker Combinations Primer Sequences
 
 
Set AIMS
Set AIMS

 

Set Year #of Markers # of Dinucleotide Markers (Fraction) # of Markers Shared with Previous set (Fraction)
1
1992
231
211 (0.91)
 
2
1993
366
347 (0.95)
131 (0.36)
3
1993
319
226 (0.71)
176 (0.55)
4
1994
347
243 (0.70)
274 (0.79)
5
1994
363
191 (0.53)
265 (0.73)
6
1995
391
55 (0.14)
186 (0.48)
7
1995
390
47 (0.12)
297 (0.76)
8
1996
387
43 (0.11)
377 (0.97)
9
1997
387
44 (0.11)
378 (0.98)
10
1999
405
49 (0.12)
313 (0.77)
11
2001
410
2 (0.01)
324 (0.77)
12
2002
408
3 (0.01)
405 (0.99)
13
2003
410
3 (0.01)
405 (0.99)
14
2004
401
13 (0.03)
393 (0.98)
15
2005
402
14 (0.03)
372 (0.93)
16
2005
401
15 (0.03)
378 (0.94)

 

Set Year # of Markers # of Dinucleotide Markers # of Markers Shared with Previous Set
51 2002
387
0
52 2003
367
0
365 (0.94)
53 2004
367
0
365 (1.0)

 

Downloadable File:

Complete list of markers for each screening set

Primers for the markers within the screening sets are available from Invitrogen both in unlabeled and fluorescent dye-conjugated forms. In screening sets 6, 7, 8 and 9, the low density set is a subset of the full (high density) set with much higher average spacing between markers. The low density set may be useful in some applications as a first pass screen of the genome. The very best quality markers from the full set were chosen for the low density set. Some of the column headings require explanation. The code column indicates whether a marker is included within the low density screening subset as designated by an "X". The "+" symbol refers to markers with alleles which differ in size from other alleles by values other than integer multiples of the repeat length. A tetranucleotide repeat marker, for example, with a (+) in the codes column will often have alleles which differ in size by 1, 2, or 3 nucleotides from other alleles. Virtually all of the markers within the current screening set are of high quality. The "cM" column refers to the approximate map position of each of the markers along each chromosome. Numbers shown in this column were obtained from new linkage maps constructed using only the markers from the screening set. The "cM between" column indicates the spacing between adjacent markers. The "allele size/bp" column indicates the size range for the amplified fragments for each marker. The "1331-01" and "1331-02" columns indicate the genotypes for these two reference individuals (parents of CEPH family 1331). DNA for these two reference individuals can be purchased from the NIGMS Human Genetic Mutant Cell Repository in Camden, New Jersey. The type and repeat length for most of the markers within the screening sets are indicated by the marker name. For example, GGAA3A07 is a CHLC "GGAA" tetranucleotide STRP on chromosome 1. Dinucleotide repeat STRPs within the screening sets can be recognized by the Genethon marker names or by the Mfd (Marshfield) marker names. The only exceptions to this rule are tetranucleotide repeat markers Mfd219, Mfd232, and Mfd238 on chromosome 19.

Marker combinations are preliminary combinations of screening set markers for simultaneous amplification and electrophoresis. The dye listed is the one that the combination was developed in, but potentially the combination could work with any fluorescent dye. All of the screening set markers are not in multiplex PCR combinations, but this work is ongoing and the list will be updated as these new combinations are developed. The goal is to be able to amplify the complete screening set in less than 100 PCR reactions.