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The Jackson Laboratory T31 Mouse Radiation Hybrid Database

The Jackson Laboratory T31 Mouse Radiation Hybrid Database includes all publicly available T31 radiation hybrid data from all sources, including the large genome centers at The Whitehead Mouse RH Database, The UK Mouse Genome Centre, and Genoscope - CNS, as well as many individual laboratories all over the world. The data are mapped together into a single comprehensive map, which is made available in these pages. We have an RH Data Submission Web interface for automated analysis of new T31 RH data, and the public data are viewable and downloadable. The automated server usually results in return email with details of the linkage analysis in less than an hour. Additional queries should be sent by regular email, and will be promptly answered. Data made public in this database will also be conveyed to MGD and to RHdb at EBI. Please check back regularly for updates: new raw data will be posted approximately every six to eight weeks. Please email questions or comments to lbr@jax.org.

There are now Mouse genome sequence assemblies from data frozen in February 2002 available from both NCBI (for the Whitehead assembly) and from Ensembl. There is a third Mouse genome sequence site at the University of California at Santa Cruz. The T31 RH map and the available sequence assemblies should be used as complementary resources to check and confirm each other, and for now we recommend using both for placing new loci on the genome maps.

For a detailed discussion of RH data and analysis issues, see in our paper Rowe LB, Barter ME, Eppig JT, 2000. Cross-referencing radiation hybrid data to the recombination map: lessons from mouse Chromosome 18. Genomics 69: 27-36.

Note this news:

December, 2002. The framework maps are now completed (find the maps by chromosome by clicking the RH Maps link at the tops of these pages). Our report on this work is in press in Genome Research (for January 2003), and an advance PDF file of the paper is already available on the Genome Research web site.

We are continuing to check the ESTs that have yet to find a BLASTN or Unigene match, and to add definitions to the database as we find them. New data submissions are still integrated into this database to keep the RH map up to date. We will continue to update the Web data approximately every two months.

For those who are contemplating mapping with the mouse Radiation Hybrid Panel, we offer this discussion:

1. We recommend that you (carefully!) re-format the radiation hybrid DNAs into microtiter format so that multichannel pipettors can be used to handle the DNAs, reducing the possibility of sample mis-ordering in each experiment.
2. If you wish to eliminate enough of the cell lines to fit a single 96-well plate, please look below for the August 1999 News item that addresses this point.
3. The order of the 100 T31 cell lines that we use is the order given by Research Genetics. The Whitehead Institute/MIT uses a different order. Below is a copy of the order we use from Research Genetics.

T31 RH set # cell line #;
1 1a12; 2 1f7; 3 1p9; 4 2b10; 5 2f12; 6 2h7; 7 2t6; 8 3f2; 9 1c1; 10 1n2; 11 1p11; 12 2b12; 13 2g1; 14 2h12; 15 2t7; 16 3f10; 17 1c2; 18 1n6; 19 2s1; 20 2t8; 21 3f9; 22 1c7; 23 1n9; 24 1p12; 25 2c2; 26 2g3; 27 2s3; 28 2t12; 29 3g3; 30 1d9; 31 1n10; 32 2a7; 33 2c3; 34 2g4; 35 2s4; 36 2l2; 37 3g4; 38 1d10; 39 1n12; 40 2a8; 41 2c4; 42 2g5; 43 1e1; 44 1o1; 45 2a10; 46 2c7; 47 2g6; 48 2s5; 49 2l3; 50 3g6; 51 1e4; 52 1o8; 53 2a11; 54 2c8; 55 2g9; 56 2s8; 57 2l4; 58 3g7; 59 1e5; 60 1o10; 61 2a12; 62 2c10; 63 2g10; 64 2t3; 65 2l6; 66 3h2; 67 1e9; 68 1o12; 69 2b3; 70 2l7; 71 3h4; 72 1e11; 73 1p1; 74 2b5; 75 2f3; 76 2g12; 77 2t4; 78 2l8; 79 3h12; 80 1f3; 81 1p3; 82 2b7; 83 2f11; 84 2h1; 85 2t5; 86 2l10; 87 3l7; 88 3l9; 89 3l10; 90 3l11; 91 3m1; 92 3m2; 93 3m6; 94 3m9; 95 3m10; 96 3m11; 97 3m12; 98 3k11; 99 3k12; 100 3l6.
4. Data confirmation and error checking. Since radiation hybrid mapping is a +/- PCR assay, false positive and false negative reactions may distort the linkage. The radiation hybrid assay standard is to do all reactions in duplicate, retype all non concordant results to determine the final correct score for each cell line. Since the majority of mouse primers also amplify one or more hamster fragments, these hamster bands may serve as a positive control in many reactions. If the hamster and mouse bands cosegregate, it becomes necessary to find a different assay for the locus. We would like investigators to tell us which assays are confirmed by the presence of a non-comigrating hamster band, and which are based on duplicate (or more) assays. Other error detection is less easy with radiation hybrids than with genetic crosses, since there is no equivalent of crossover interference. We suggest rigorously retyping any lines that give a new (-) in a string of previously linked (+), or vice versa, or that show a weaker positive signal, especially when next to a strong positive lane. Where we receive two or more different scorings for the same locus, we will need to base the map on one result or the other, and will need to use the relative thoroughness of the error checking as our guide in this choice.
5. We have investigated some of the cases of discordant typings for the same locus in our own laboratory. By repeating the assays using the reported protocols, our results show few disagreements in data reading. However, the different PCR and/or gel protocols used by the different investigators result in differing data in our own hands for a significant number of the cell lines. These results lead us to suggest that, at least for the typing of the D_Mit_ anchor loci using commercial primers, a reasonable standard protocol should be used by all. We suggest a protocol that is easy and fast, highly sensitive, and robust. After testing several protocols in our own laboratory we recommend using the following conditions:

PCR cycling: 94 degrees 3 minutes, (94 degrees 30 seconds, 55 degrees 35 seconds, 72 degrees 30 seconds) 38 times, 72 degrees 7 minutes, 4 degrees hold.

Gel systems: use very sensitive detection conditions, such as radioactive products on thin acrylamide gels, or thin high concentration agarose gels stained with ethidium bromide and illuminated with 254 nm or with SYBR Green (FMC) and illuminated with 300 nm UV light.

6. For the best internally consistent linkage information, we recommend that new data include several flanking markers within a narrow genomic region. Data obtained within a single laboratory using consistent methods appear to give the best fit.
7. Investigators are finding, and we can confirm in our own laboratory, that CA-repeat loci like the D_Mit_ markers sometimes show allelic variation within the T31 cell lines. It appears that the length of such simple sequence repeats is more unstable in the growth of the cell lines than in the genomes of living animals, perhaps more similarly to what is observed in tumors. We find that scoring from one primer pair all non-hamster band sizes as a single locus usually gives the best fit to surrounding RH data.
8. In addition, the intensity of positive signals varies greatly from one cell line to another (probably due to the process of the gradual loss of the mouse DNA fragments from the host cell line karyotype), and that all faint signals should be read as positive unless they are otherwise questionable (fuzzy bands or similar to hamster bands).

Older news items:

November, 2002. A few additional changes have been made in the marker order to improve the cR linkage. The framework maps are now completed, and our report on this work is in press in Genome Research (for January 2003).

We are continuing to check the ESTs that have yet to find a BLASTN or Unigene match, and to add definitions to the database as we find them. 134 new EST definitions have been added in this posting.

October, 2002. A few additional changes have been made in the marker order to improve the cR linkage. An additional 43 functional definitions are associated with EST loci mapped on Chr 6, indicated in our Alias column in the RH Data pages. 16 new MIT SSLP markers have been added.

We have added 16 new SSLP anchor markers to the T31 RH map: D3Mit107, D3Mit123, D3Mit345, D3Mit361, D4Mit83, D7Mit130, D7Mit183, D7Mit203, D9Mit126, D9Mit294, D9Mit326, D11Mit293, D12Mit111, DXMit244, DXMit246, and DXMit248.

We are continuing to check the ESTs that have yet to find a BLASTN or Unigene match, and to add definitions to the database as we find them.

August, 2002. An additional 162 functional definitions are associated with mapped EST loci on Chrs 3, 4, and 5, indicated in our Alias column in the RH Data pages. 27 new MIT SSLP markers have been added.

We have added 27 new SSLP anchor markers to the T31 RH map: D1Mit175, D1Mit237, D1Mit311, D3Mit68, D3Mit106, D3Mit343, D4Mit107, D4Mit142, D4Mit195, D5Mit227, D5Mit268, D5Mit381, D5Mit388, D6Mit194, D7Mit96, D7Mit244, D11Mit49, D10Mit215, D11Mit31, D11Mit60, D11Mit89, D11Mit203, D11Mit298, D11Mit303, D11Mit317, D12Mit112, D16Mit46. We also remapped 6 additional SSLP markers to improve the fit of the data to the surrounding map.

July, 2002. An additional 375 functional definitions are associated with mapped EST loci, indicated in our Alias column in the RH Data pages. 33 more ESTs have been renamed with functional gene names. Note that all the RH-mapped ESTs have now been checked for functional association by BLASTN at least once.

We have added 13 new SSLP anchor markers to the T31 RH map: D1Mit375, D3Mit54, D4Mit9, D4Mit212, D4Mit230, D4Mit296, D6Mit220, D10Mit52, D10Mit191, D10Mit252, D11Mit275, D11Mit316, D12Mit126. We also remapped 7 additional SSLP markers to improve the fit of the data to the surrounding map.

May, 2002. We have updated the framework maps that correlate the genetic data from The Jackson Laboratory Backcross DNA panels with the T31 RH mapping data, and added several new chromosome maps. These maps reflect the latest revisions in our RH map and the most recent backcross data. We expect to complete the rest of the chromosome framework maps in the near future.

We have recently updated the database of anchor markers that underlies our automated RH data analysis server. This update should improve the accuracy of results from the RH Data Submission mapping server. In the May data posting, an additional 248 functional definitions are associated with mapped EST loci, indicated in our Alias column in the RH Data pages.

March, 2002. A few "shakedown" changes have been made in the marker order that we posted in January. A batch of 242 additional EST loci from the laboratory of Roger Cox have been added to our RH map. An additional >400 functional definitions are associated with mapped EST loci, indicated in our Alias column in the RH Data pages.

There were 30 of the 242 data sets from Roger Cox's group that we retrieved from the Genoscope Web site that failed to make the LOD of 6 cut-off for significant linkage, and these are not included in the maps posted here. A complete list of the new Cox EST markers that failed to reach the LOD 6 criterion is below:

AU021184, AU021095, AU021075, AU020844, AU020837, AU020805, AU020544, AU020152, AU020151, AU020091, AU020046, AU019997, AU019986, AU019910, AU019409, AU019380, AU019264, AU019190, AU019186, AU019139, AU019138, AU019121, AU019098, AU019084, AU019038, AU018547, AU018447, AU018409, AU018388, AU018326

There are eight EST markers that, when mapped by two different research groups, matched two different map locations. We wondered whether these discrepancies were likely to be due to primer mixups or were indicative of related sequences that are unlinked in the genome. To retrieve additional relevant information about these EST loci, we tried BLASTN against the Ensembl mouse genome sequence assembly. [Note that there is also a BLAST server for the WGS assembly of mouse sequence at NCBI.]

AA409043 matched best (e-52) to proximal Chr 15 and (e-40) to proximal Chr 7. Genoscope RH data place this EST locus on proximal Chr 7 with misfitting scores that match the Chr 15 location well. Thus it appears that the Genoscope assay for this EST locus generated positive scores from two related loci whose map positions are concordant with two related sequences in the Ensembl sequence assembly. The UK Mouse Genome Centre RH mapping data for this same EST fit best on our Chr 4 map, and the only Ensembl BLASTN hits on Chr 4 for this marker are very low match (0.41). Thus we suspect that there may either have been a record keeping error in this mapping or a missing sequence in the assembly.

C76435 data from the UK Mouse Genome Centre fit our RH map on distal Chr 8, and the misfitting scores in this position mapped to Chr 10. Data for the same EST from the Whitehead Institute maped cleanly to the same Chr 10 location. The Ensembl BLASTN for this EST matched best (e-57) to distal Chr 8, and there is no match (yet?) to the Chr 10 sequence data.

C78353 data from the UK Mouse Genome Centre fit well on proximal Chr 9, whereas data for the same EST from The Whitehead Institute fit distal Chr 17. The Ensembl sequence assembly shows a top BLASTN hit (e-96) to a similar position on distal Chr 17, and another very high BLASTN match (e-82) on proximal Chr 9, confirming both of these map positions.

AA407142 data from the UK Mouse Genome Centre fit well on proximal-central Chr 7, whereas data for the same EST from Genoscope fit central-distal Chr 8. The Ensembl sequence assembly shows a top BLASTN hit (e-70) to a similar position on Chr 7, and another very high BLASTN match (e-67) on a similar location on Chr 8, confirming both of these map positions.

Two map positions for AA408005 were similarly supported by the sequence assembly.

Three other ESTs, AU019308, C81120, and AA407276, also map to two different map locations one of which agrees with a high homology BLASTN hit in the Ensembl assembly and the other of which has no evidence of a corresponding sequence assembly match. These may be indicative of missing information in the sequence assembly, errors in the assembly, or errors in the mapping labs.

In general, we found the Ensembl sequence assembly to be easy to access and helpful in our analyses. Using these two resources, the T31 RH map and the available sequence assemblies, to check and confirm each other is a useful exercise, and for now we recommend using both for placing new loci on the genome maps.

January, 2002. The curation of the Whitehead Release 10 data and the Genoscope Fall 2001 release has been completed. The entire T31 RH map has been recalculated based on the current 24,983 data sets. The recalculation of the maps resulted in an almost 10% reduction in the overall map lengths due to improved fit of locus order. There are many small changes in local order compared to previous map versions, and only a few more major changes such as inversion of groups of loci.

There were 102 of the 4035 Genoscope Fall 2001 release data sets that failed to make the LOD of 6 cut-off for significant linkage, and these are not included in the maps posted here. A significant number of these appear to have a very high retention frequency (of 60 to 100 percent) but do not link to distal Chr 11. A complete list of the CNS Genoscope EST markers that failed to reach the LOD 6 criterion is below:

AL118141, BB364858, AA472867, AA387896, AA123324, AA607238, AV174254, AA122643, AA547390, AL024155, AA009215, AA032457, AA096908, AA103344, AA114686, AA117441, AA162693, AA117357, AA117985, AA104438, AA008714, AA000171, AA163561, AA125090, AA166540, AA008830, AA422805, AA472872, AA589966, AA624189, AA693064, AA537416, AL024122, AA549402, AL024431, AL024419, AL118290, AV357345, AL024135, AL024192, AL024182, AA690052, AL024206, AL024376, AL117721, AL024333, AA544928, AA545652, AI464189, AA511901, AA172569, AL118045, AL024434, AA387155, AA388631, AA388716, AA399914, AA170959, AA410172, AA414084, AA414815, AA432744, AA437767, AA438018, AA450448, AA450839, AA465888, AA465954, AA466746, AA467160, AA473931, AA545274, AA547219, AA560849, AA575001, AA608162, AA671413, AA681305, AA681311, AA681366, AA683709, AA684416, AA691037, AA755286, AI427072, AI427140, AI428488, AU016926, AU022871, AV050757, AV095376, AV129124, AV145838, AV299486, AV299594, AV300198, AV302804, AV309259, AV352810, AV357485, AA422784, AA003797

The apparent (slight) contraction in the size of the database from the 24,991 data sets in the October 2001 posting to the 24,983 in the January 2002 posting reflects our discovery that our software missed 161 duplicate data sets from the Whitehead Release 10 that we had already included from previous releases. The Release 10 included 1434 newly mapped ESTs, not the 1595 we originally reported.

Five of the Whitehead new Release 10 EST loci appear to map to a different chromosome than the one to which the Whitehead Institute has assigned them:

• BB317391 (LOD 26) and BB315977 (LOD 19) map to Chr 15, while Whitehead lists these on Chr 10.
• BB402489 maps to Chr 19 with a borderline LOD score of 6.5, while the Whitehead lists it on Chr 1.
• AA987181 (LOD 9.7) and BB137539 (LOD 22) map to Chr 6 while the Whitehead lists these on Chr 9. Note that AA987181 is an EST for Hoxa9 which has been mapped to Chr 6 by other methods, and is also mapped to the same Chr 6 position in this T31 RH panel by another laboratory.

January, 2002. Happy New Year. For anyone who is looking for a new posting of our RH data, it is coming soon. The reason for the delay is two-fold. Firstly, there have not been any large new data sets made available since our October posting. So, secondly, we have taken this opportunity to complete the curation of the more than 5000 most recently added EST mapping data sets, and to recalculate the maps. Look for a new posting of the data later this month.

October, 2001. The most recent RH data release contains 185 new MIT anchor locus data sets from the latest Release 10 from the Whitehead Institute and an additional 1595 new EST mapping data sets from that release.  In addition, we have added 3944 more EST locus mapping data sets recently released by the Genoscpoe - CNS group. All of these newly mapped EST loci are assigned provisional placement only at this time, and are flagged with "@w- " (Whitehead Release 10) and "@g-" (Genoscope Fall 2001 release) before the locus names in our data displays to distinguish these from other loci whose position has been more completely curated.

The new MIT anchor marker data included eight loci that map in conflict with the original genetic map position posted at the Whitehead Genome Map site.  These are D13Mit67 that is confirmed to map on Chr 10, D18Mit223 that is mapped on Chr 13 (and also on Chr 11), D5Mit109 confirmed on Chr 1, D5Mit34 newly placed on Chr 16, D1Mit129 newly placed on Chr 5, D9Mit170 newly placed on Chr 6, D9Mit92 newly placed on Chr 8, and D7Mit36 newly placed on Chr 12. Please recognize that apparently mismapping MIT markers may be due to primer labeling problems at Research Genetics or handling mixups in the mapping laboratory. Not until a locus has been mapped over time by several independent laboratories or if the position is confirmed by sequencing can the distinction be made whether the newer mapping or the original chromosomal assignment is in error.

We have added new functional annotations from BLASTN and Unigene. In addition, 64 newly published genes are included in this posting.

Note: the inclusion of an MGI locus symbol in our Alias column is not proof of identity, but is meant as a guide to those searching for possible functional association.

The current RH map statistics:

In the currently posted RH data set there are 24,991 marker data sets. This includes some redundancy, as there are some loci that have been mapped by two or more independent laboratories, and the data for each are listed separately.

There are 18,945 EST data sets that define loci on the map with sequence accession numbers. The degree of redundancy associated with the 5539 new ESTs from the Whitehead and Genoscope has not yet been determined. 5098 ESTs are associated with functional information by high BLASTN or Unigene match to known genes. There are now 404 additional genes mapped as cDNAs with full gene identification.

There are 5904 STS loci, of these 5799 are the D-Mit- SSLP anchor markers, but this number includes 1900 "redundant" data sets so there are currently 3892 different MIT markers mapped in the T31 RH panel.
 

For a detailed discussion of RH data and analysis issues, see in our recent paper Rowe LB, Barter ME, Eppig JT, 2000. Cross-referencing radiation hybrid data to the recombination map: lessons from mouse Chromosome 18. Genomics 69: 27-36.

August, 2001. The big news event of the mouse RH mapping database is the recent (16 August) load of 11,927 new markers into MGD from EST loci mapped in The Jackson Laboratory T31 RH Database. The arrival of this large number of T31 RH-mapped sequences in MGD brings the total number of genetic markers in MGD to over 50,000.

Seqid   MGI:ID for marker   MGI gene symbol   Chr (MGI)   Chr (RH)

AA408841   MGI:1353622   AA408841   6   1
AF089869   MGI:1313271   Stk16   11   1
C78743   MGI:1261792   D10Ertd203e   10   1
U35035   MGI:106591   Matn1   4   1
U36575   MGI:102463   Nfatc2   2   1
AF019926   MGI:1347559   Stk22b   16   2
AI316844   MGI:1353641   AI316844   14   2
AU022948   MGI:1261849   D5Ertd579e  5   2
R74979   MGI:107886   Rpn2-rs1   7   2
AF006196   MGI:1333882   Adam15   1   3
AF123611   MGI:1354945   Ppap2c   10   3
AU014956   MGI:1277099   D19Ertd626e   19   3
R75386   MGI:106255   D19Bwg0552e   19   3
R74925   MGI:107765   Apbb1   7   4
AJ001261   MGI:1278343   Gbas   4   5
D21061   MGI:101909   Gpcr12   4   5
U81829   MGI:1097158   Calu   7   6
AU014580   MGI:1277233   D17Ertd599e   17   7
AU022685   MGI:1261790   D2Ertd554e   2   7
R74827   MGI:107274   D10Bwg0134e   10   7
U77083   MGI:96749   Anpep   9   7
X74616   MGI:97576   Phka1   X   7
C78460   MGI:1098578   D17Ertd178e   17   8
C79612   MGI:1098752   D4Ertd274e   4   9
X06340   MGI:88356   Cdh3   8   9
C76412   MGI:1098798   D6Ertd14e   6   10
D31898   MGI:109559   Ptprr   8   10
R75170   MGI:106430   D8Bwg1112e   8   10
X54149   MGI:107776   Gadd45b   9   10
AA408617   MGI:107648   D1Wsu158e   1   11
AJ001260   MGI:1278344   Nipsnap1   4   11
L06039   MGI:97537   Pecam   6   11
N28086   MGI:106426   D8Bwg1414e   8   11
AU014900   MGI:1277232   D2Ertd623e   2   12
C79947   MGI:1098811   D1Ertd291e   1   12
AB002664   MGI:97284   Ncf2   1   13
C79927   MGI:1098810   D4Ertd290e   4   13
D88611   MGI:108044   Gcm1-rs2   10   13
D32072   MGI:98729   Tgfbr2   9   16
J04634   MGI:103190   Ly64   13   16
U07861   MGI:107547   Zfp101   7   17
X00876   MGI:98834   Trp53   11   17
AF026481   MGI:95298   Eif1a   12   18
C79589   MGI:1098694   D15Ertd271e   15   18

We have added new functional annotations from BLASTN and Unigene, bringing the total number of mapped ESTs with some functional association so far to 4,930. In addition, 54 newly published genes are included in this posting.

Note: the inclusion of an MGI locus symbol in our Alias column is not proof of identity, but is meant as a guide to those searching for possible functional association.

The current RH map statistics:

In the currently posted RH data set there are 19,191 marker data sets. This includes some redundancy (see below), as there are some loci that have been mapped by two or more independent laboratories, and the data for each are listed separately.

There are 13,406 EST data sets that define 12,199 unique EST or cDNA loci on the map with sequence accession numbers. 4930 of these are associated with functional information by high BLASTN or Unigene match to known genes. 655 of these are cases of multiple mapped ESTs matching the same gene. 91 new associations have been made between mapped ESTs and RIKEN full length cDNAs; a total of 3924 RIKEN clone IDs are associated with 2642 of these RH mapped EST markers. There are 643 other EST loci mapped without sequence accession number information. There are now 340 additional genes mapped as cDNAs with full gene identification.

There are 5688 STS loci, of these 5583 are the D-Mit- SSLP anchor markers, but this number includes 1799 "redundant" data sets so there are currently 3784 different MIT markers mapped in the T31 RH panel.

June, 2001. We have added new functional annotations from BLASTN and Unigene, bringing the total number of mapped ESTs with some functional association so far to 4,805. 161 new mapped ESTs and 64 newly published genes are included in this posting.

Note: the inclusion of an MGI locus symbol in our Alias column is not proof of identity, but is meant as a guide to those searching for possible functional association.

There are newer framework map graphics for Chromosomes 1 and X. Look for additional chromosome frameworks coming soon.

The current RH map statistics:

In the currently posted RH data set there are 19,122 marker data sets. This includes some redundancy (see below), as there are some loci that have been mapped by two or more independent laboratories, and the data for each are listed separately.

There are 13,406 EST data sets that define 12,199 unique EST or cDNA loci on the map with sequence accession numbers. 4805 of these are associated with functional information by high BLASTN or Unigene match to known genes. 655 of these are cases of multiple mapped ESTs matching the same gene. 3833 RIKEN clone IDs are associated with 2551 of these RH mapped EST markers from the paper in Nature 409 (2001). There are 643 other EST loci mapped without sequence accession number information. There are 305 additional genes mapped as cDNAs with full gene identification.

There are 5652 STS loci, of these 5548 are the D-Mit- SSLP anchor markers, but this number includes 1790 "redundant" data sets so there are currently 3758 different MIT markers mapped in the T31 RH panel.

May, 2001. We have added new functional annotations from BLASTN and Unigene, bringing the total number of mapped ESTs with some functional association so far to 4,588 (35.6% of the mapped ESTs).

Note: the inclusion of an MGI locus symbol in our Alias column is not proof of identity, but is meant as a guide to those searching for possible functional association.

Two newly mapped MIT markers failed to map on the expected chromosome: D12Mit152 was mapped to Chr 17 by Purcell et al., and D1Mit59 has now been mapped to Chr 10 independently by three different groups using both this RH panel and TJL BSS/BSB backcross panels.

Our laboratory is involved in building the complete genome framework map by choosing markers at LOD > 6 intervals from the RH data to map onto TJL BSS/BSB panels for order confirmation and distance comparison. As our frameworking efforts continue, the marker order in this RH map is being corrected by reference to the improving detail from the backcross maps. We recently uncovered evidence for error in the consensus map for proximal Chromosome 1. The RH locus order on the proximal end of Chromosome 1 has been corrected to reflect the new information from the proximal part of TJL BSB map, and the actual sum of the breaks necessary to explain the locus order in the RH map has been reduced thereby. We anticipate that more of these kinds of locus order problems will come to light as the framework comparison between the backcross maps and this RH map continues to develop.

The current RH map statistics:

In the currently posted RH data set there are 18,902 marker data sets. This includes some redundancy (see below), as there are some loci that have been mapped by two or more independent laboratories, and the data for each are listed separately.

There are 12,882 EST data sets that define 12,035 unique EST or cDNA loci on the map with sequence accession numbers. 4588 of these are associated with functional information by high BLASTN match to known genes. 3833 RIKEN clone IDs are associated with 2551 of these RH mapped EST markers from the paper in Nature 409 (2001). There are 643 other EST loci mapped without sequence accession number information. There are 241 additional genes mapped as cDNAs with full gene identification.

There are 5607 STS loci, of these 5544 are the D-Mit- SSLP anchor markers, but this number includes 1789 "redundant" data sets so there are currently 3755 different MIT markers mapped in the T31 RH panel.

March, 2001. Where relevant, we have added RIKEN full length cDNA SeqIDs and CloneIDs to the notes for the mapped ESTs. There are also additional functional annotations from BLASTN and Unigene, bringing the total number of mapped ESTs with some functional association to 4,487. New annotation has been added to the RH data pages to alert users to ESTs that have functional information without MGI locus symbols.

New functional annotation: We now have MGI locus symbols associated with 3388 of the mapped ESTs, and include our criteria for these assignments in the notes field for each locus. Since there are 1076 additional ESTs with some functional association but without approved mouse locus symbols, we have added a tilde (~) to the Alias column on the data pages for those ESTs to alert users to look for the defining information in the notes (click on the hypertext locus names to view the references and notes). The addition of functional annotation is an ongoing process, and new definitions and locus symbols will be added as we find them.

Note: the inclusion of an MGI locus symbol in our Alias column is not proof of identity, but is meant as a guide to those searching for possible functional association.
 

January, 2001. The latest posting contains 159 additional EST loci from The UK Mouse Genome Centre, and many new definitions for mapped EST loci. Look also for the framework maps being added to the RH Maps link at the top of these RH Database pages.

We have continued to search for BLAST matches and have also added Unigene ids for some ESTs that are mapped in this T31 panel. In this posting there are 12,885 mapped EST loci of which 2,867 are associated with MGI locus symbols and an additional 1,098 ESTs have functional definitions without MGI locus symbols. This process of adding annotation to the mapped ESTs is ongoing, and more will be added in future postings along with any new mapping data that becomes available.

Note: the inclusion of an MGI locus symbol in our Alias column is not proof of identity, but is meant as a guide to those searching for possible functional association.

Under the RH Maps link at the top of the RH Database pages you can now find images of our framework maps in progress.  We are building a framework map of known-order anchor markers between the mouse T31 radiation hybrid (RH) panel and the recombination map based on The Jackson Laboratory (TJL) interspecific backcross panels using the established genetic order to evaluate and strengthen the RH results. We have so far posted frameworking maps for 6 of the 20 mouse chromosomes, and continue to work on the remaining chromosomes. The next chromosome to be completed will be the X Chromosome, followed by Chromosome 1.

Radiation hybrid maps to date have been constructed based on analysis of the radiation hybrid data using minimum break and maximum likelihood algorithms.  The resulting map order can be compared to the available genetic recombination data for evaluation of the accuracy of the calculated marker order.  Discordance between the two orders reveals problems either in the genetic recombination data or in the radiation hybrid data or analysis. The Jackson Laboratory (C57BL/6JEi x SPRET/Ei)F1 X SPRET/Ei (BSS) and (C57BL/6J x M. spretus)F1 X C57BL/6J (BSB) panels constitute a resource of 188 backcross animals that are completely typed for thousands of markers.  These panels are readily available for additional marker typing, and hundreds of the D-Mit- SSLP anchor loci have been mapped on these panels.  The panel data are robust because complete progeny typing allows any suspected errors that may distort the genetic map to be identified easily and rechecked as needed. The complete raw data and maps from this cross are in a community database on the Web site (http://www.jax.org/resources/documents/cmdata ).

In high density recombination mapping data, crossover interference means that single-locus double crossovers are almost always errors and these are easy to identify and retype.  In addition, typing backcross DNAs for PCR-based polymorphism results in clear strong single-copy bands from all samples so that PCR artifacts affecting a few samples are very easy to detect.  Thus, all mapping assays are highly reproducible and can be readily confirmed or corrected. The same level of certainty is not so easily achieved with RH typing.  Some of the problems inherent in data gathering methods that are common to all RH mapping are: (1) mouse-specific band intensity variation, (2) a relatively high frequency of microsatellite allele differences among the RH cell lines, (3) a 0-10% rate of discordance between duplicate assays, (4) artifactually high (PCR conditions too permissive) or low (PCR conditions too restrictive, or insufficient sensitivity of PCR product detection conditions) retention frequency, (5) comigrating hamster and mouse PCR products, (6) discordance between results using the same primers in different laboratories or different PCR protocols.   All of these problems can be addressed by careful attention to the techniques used in RH typing (see suggestions below).  In addition to these problems, there are difficulties in data interpretation and map building: (1) a given cell line often contains multiple apparently discontinuous segments retained from a given chromosome, making data error detection and locus ordering unclear, (2) inserting new locus data sets most often expands the map, making estimates of physical distance appear to depend on marker density, (3) ambiguous or missing data reduce the significance of neighboring linkages, and (4) nearby loci may have up to a two-fold difference in retention frequency, making some gaps in the map difficult to close.

We are using the TJL BSS and BSB crosses to definitively order at a maximum resolution of 0.5 cM D-Mit- SSLP anchor loci that are mapped on the T31 mouse whole genome radiation hybrid panel (McCarthy et al., 1997), so as to link the two maps at intervals that are supported with significance (LOD > 6) by the T31 panel data. We are continuing to cross-reference the RH data to the TJL backcross data for all the mouse chromosomes to improve further the power of RH mapping and to more precisely integrate the extensive existing recombination mapping data for the mouse with the incoming radiation hybrid map data.
 

December, 2000. The latest posting contains 409 additional MIT anchor loci mapped at Genoscope - CNS, and 1,870 new EST loci.

There are 409 new MIT marker data sets from the Genoscope-CNS project included in this posting. Not all of these are new markers to the overall database. Two of these mapped to locations that are discordant with their locus names:

D17Mit264 maps to Chromosome 4, LOD 10.0 to D4Mit237.
D8Mit46 maps to Chromosome 9, LOD 15.1 to D9Mit214, in the same location as two previous versions of this locus.

D7Mit190,
D11Mit289,
D11Mit285,
D11Mit179.

More notes on the MGI locus symbols listed in the Alias column in the data display. We have included in the locus notes (accessed by clicking on the hypertext  locus name in the data display) the basis on which we associated each EST with an MGI locus symbol. If the BLAST match was e -100 or smaller, we state that the EST sequence "matches" the MGI locus, and if the MGI locus already has a chromosomal assignment, the location has to be to the same chromosome. If the chromosomal assignment is in conflict with previous data in MGD, we mark the alias name with a "?". If the BLAST match was e -100 to e -50, we state that the EST is "similar to" the sequence associated with the MGI locus. Thus, the inclusion of an MGI locus symbol in our Alias column is not proof of identity, but is meant as a guide to those searching for possible functional association.

October, 2000. The latest posting of T31 RH data includes updated EST mapping data ***and a new format feature to assist those whose interest is in more functional aspects of genomics: MGI locus symbols***

There are now 9509 ESTs mapped in the T31 RH data set. We are in the process of adding the MGI locus symbols to the EST notes where these are available. We have added locus names where these are available for about half of the ESTs on the map, and the rest of the names will be added in the next data release due at the beginning of December.

***new format feature: on the data display pages, we have added a new column next to the primary locus name that shows the functional gene MGI locus symbol associated with the mapped ESTs. This column is headed "Alias" to indicate that it includes alternate locus names. Note that all locus names not preceded by #-signs (except the temp### designations) are approved mouse locus names that can be used to search MGD for additional information. Our reasoning for keeping the sequence accession numbers as our primary locus names is that multiple accession numbers may be attached to the same functional gene (there are already many examples of this), and sometimes these may legitimately map in a specific order, eg. if two mapped sequences are at far ends of large functional units. Where the data support it, we have ordered the data vectors for the same functional gene adjacent to each other. In most cases there is no or only marginal preference in the data for a specific order of the multiple ESTs for the same gene. There are a few cases where the data could not support such proximity. The best example to date is Catna1 on Chr 18 as AA517462, data from Genoscope, and AI988031, data from Whitehead Institute Release 5. These cases may indicate one or more technically flawed data sets, misassignment of the gene identity to one or both ESTs, or that some or all of the intervening markers may also be from the same gene or other genes whose sequence appears in introns or as alternate splice forms of the gene represented by the separated markers.

We have also added more hot links in the notes for many loci, to take you directly to the sources of additional information.

For a detailed discussion of RH data and analysis issues, see in our recent paper Rowe LB, Barter ME, Eppig JT, 2000. Cross-referencing radiation hybrid data to the recombination map: lessons from mouse Chromosome 18. Genomics 69: 27-36.

August, 2000. The latest posting of T31 RH data includes updated EST mapping data

 There is now available EST data for Release 7 from The Whitehead Institute, and we are currently mapping these new markers into this comprehensive database. In the meantime these data are available on the Whitehead Web site. Additional EST data from the MRC and the Genoscope - CNS are expected to be released by those groups near the end of September.

We have also added new convenient hot links in the notes for many loci, to take you directly to the sources of additional information.

July, 2000. The latest posting of T31 RH data includes updated EST mapping data

 Important note: this posting also includes repair of the mapping of the Whitehead Institute's Release 2 EST data on Chromosomes 8 and 11. We discovered that the marker names and data vectors were misaligned in our May posting. This problem affected the Release 2 EST data on these two chromosomes ONLY.

 There is now available EST data for Release 5 from The Whitehead Institute, and we are currently mapping these new markers into this comprehensive database. In the meantime these data are available in the Whitehead Web site.

May, 2000. The latest posting of T31 RH data includes updated EST mapping data

The ESTs are listed with their sequence accession numbers as locus names where these are available, except for those loci already assigned an approved mouse locus name, such as the D-Wsu- and D-Ertd- EST loci that are also mapped in the Jackson Laboratory BSS interspecific backcross. As usual, unapproved locus names are preceded by a # sign.

 There are many cases of the same EST mapped by different laboratories, and these are listed adjacent to each other if the data are similar enough to justify this proximity. The version of the data that fits the surrounding data with the highest LOD is marked with an asterisk (*), and is the version used by us in map building.

 There were 83 of the 1480 EST loci from CNRS that failed to match the available data with a LOD greater than 6. A few of these had a convincing enough match to include in the map at the lower LOD, but 63 loci with low LODs are left off the map. These are:

 AA022664, AA024112, AA024335, AA407614, AA408003, AA408315, AA408610, AA408811, AA409062, AA409343, AA409501, AA409859, AA410062, AA410107, AA420378, AA516950, AA536813, AA536868, AA545169, AA545203, AA545210, AA589482, AA589500, AA673422, AL022642, AL022651, AL022682, AL022753, AL022776, AL022795, AL022802, AL022825, AL022881, AL022904, AL022965, AL023993, AL024064, AL024067, AL024117, AL024139, AL024151, AL024208, AL024214, AL024250, AL024254, AL024259, AL024290, AL024351, AL024373, AL024393, AL024426, AL024429, AL033297, AL033303, AL033310, AL033345, AL033368, C81232, R74721, R75026, R75161, W51703, W91703

 There were 15 of the 1938 EST loci from the MRC that failed to match the available data with a LOD greater than 6. These are:

 AA407502, AI607400, C76799, C76855, C76868, C77032, C77033, C77035, C77955, C78131, C79093, C80064, C80251, C85795, D8Ertd130e (C77044).

March 2000. The March posting of RH data includes some of the EST mapping data recently posted by the Genome Group at MRC.

In addition there are some markers posted at The Whitehead in February without definitions or documentation that have (unapproved) locus symbols in the format #M##### and #M###-###. We started to include these in our comprehensive database but then noticed that many of these data sets contained an apparent frameshift in the data for the last 10 cell lines, making the fit to the rest of the data problematic. Staff at The Whitehead promised to rectify this error in their next release. Thus we have stopped loading these data until this posting error is repaired. The Whitehead Institute made a second release March 30, so we hope to be able to include their new and repaired data in our next posting. In the meantime, for access to the newly released data have a look at the Radiation Hybrid Maps TEXT files at The Whitehead Mouse RH Database.

January 2000. The January posting of RH data does not yet include the EST mapping data recently posted by the Genome Group at MRC or the EU Consortium Group.

The January posting of RH data includes new symbols (a, b suffixes) to indicate D_Mit_ loci that have two conflicting map positions.

November 1999. The November posting of RH data includes the 1752 loci of microsatellite marker data from Genoscope in France (Philip Avner, PI) retrieved from EBI September 1999. Note that 1037 of these microsatellite markers were already represented in the database by previous data from other labs, so 715 of the loci in this set were new.

 
D1Mit280 maps to Chromosome 3*, LOD 4.9 to D3Mit110.
D1Mit329 maps to Chromosome 17, LOD 19.1 to D17Mit2.
D1Mit59 maps to Chromosome 10*, LOD 17.4 to D10Mit109.
D2Mit278 maps to Chromosome 4, LOD 10.4 to D4Mit362 (note the Whitehead mapping of this same locus fits Chr 2).
D2Mit330 maps to Chromosome 1, LOD 10.5 to D1Mit430.
D3Mit112 maps to Chromosome 12, LOD 12 to D12Mit145.
D3Mit145 maps to Chromosome 13, LOD 9.1 to D13Mit113.
D3Mit217 maps to Chromosome 1*, LOD 13.4 to D1Mit76.
D4Mit134 maps to Chromosome 14, LOD 14.1 to D14Mit132.
D4Mit78 maps to Chromosome 12, LOD 15.2 to D12Mit41.
D5Mit109 maps to Chromosome 1, LOD 16.1 to D1Mit128.
D5Mit116.1 maps to Chromosome 2, LOD 14 to D2Mit15.
D5Mit418 maps to Chromosome 9, LOD 14.0 to D9Mit61.
D6Mit73 maps to Chromosome 1, LOD 18.5 to D1Mit322.
D6Mit171 differs from Roswell Park position for the same locus on Chromosome 6.
D7Mit221 maps to Chromosome 2, LOD 15.2 to D2Mit75.
D7Mit252 maps to Chromosome 1, LOD 12.2 to D1Mit121.
D8Mit112 maps to Chromosome 9, LOD 10 to D9Mit205.
D8Mit351 maps to Chromosome 10*, LOD 15.1 to D10Mit166.
D10Mit45 maps more proximally than Whitehead's D10Mit45.
D10Mit44 maps to Chromosome 1, LOD 16.8 to D1Mit119.
D12Mit93 maps to Chromosome 17*, LOD 13.6 to D17Mit39.
D13Mit288 maps to Chromosome 16, LOD 15.1 to D16Mit132.
D14Mit169 maps to Chromosome 9*, LOD 12.6 to Tmod2.
D16Mit97 maps to Chromosome 10, LOD 10.8 to D10Mit298.
D17Mit102 maps to Chromosome 2, LOD 15.3 to D2Mit289.
D17Mit144 maps to Chromosome 11, LOD 58.8 to D11Mit27.
D17Mit163 maps to Chromosome 4*, LOD 14.2 to D4Mit289.
D17Mit85 maps to Chromosome 12, LOD 10.6 to D12Mit275.
D18Mit136 maps to Chromosome 9, LOD 14.7 to D9Mit43.
D18Mit223 maps to Chromosome 11*, LOD 15.4 to D11Mit164.
DXMit215 maps to Chromosome 4*, LOD 19 to D4Mit238.
DXMit227 maps to Chromosome 6, LOD 13.9 to D6Mit229.

August 1999. Since the RH data are now dense enough to support linkage throughout the genome, we offer our suggestion as to which cell lines to omit from typing to make a 96-sample set for more efficient typing.

line 32, has the fewest positive scores (69) in 3 small fragments of Chr 1, 1 fragment of Chr 3, 1 fragment of Chr 5, 1 fragment of Chr 6, 1 fragment of Chr 7 (proximal), 1 fragment of Chr 9, 3 fragments of Chr 10, 1 fragment of Chr 11 (distal), 3 fragments of Chr 13.

line 62, has only 86 positive scores in 1 fragment of proximal Chr 3, 1 fragment of proximal Chr 8, 1 small fragment of Chr 9, 1 fragment of Chr 11, 2 fragments of Chr 14, 1 fragment of Chr 18, 2 fragments of proximal X.

line 12, has 145 positive scores in 1 small fragment of Chr 4, 1 fragment of Chr 5, 1 fragment of Chr 6, 3 fragments of Chr 7, 1 fragment of Chr 9, 2 small fragments of Chr 10, 3 fragments of Chr 12, 1 fragment of Chr 13, 1 fragment of Chr 14, 1 small fragment of proximal Chr 15, 4 fragments of Chr 16, 2 fragments of Chr 17, 4 small fragments of Chr 19.

line 44, shows 250 "hits". Note this was one of the lines omitted by Whitehead/MIT, so this line is not as thoroughly characterized, and may contain fragments that are not detected by the smaller data set available for the line. Detected fragments are 2 fragments of Chr 7, 1 small fragment of Chr 8, 1 fragment of Chr 10, 2 fragments of Chr 13, 1 fragment of Chr 16, 1 large fragment of Chr 18.

line 11, has 263 positive scores in 3 fragments of Chr 3, 6 fragments of Chr 4, 1 small fragment of Chr 5, 3 small fragments of Chr 6, 4 fragments of Chr 7, 2 small fragments of Chr 8, 2 small fragments of Chr 9, 2 fragments of Chr 10, 2 fragments of Chr 13, 1 fragment of Chr 15, 3 small fragments of Chr 16, 1 fragment of Chr 18, 5 fragments of Chr 19.

line 46, has 263 positive scores in 2 small fragments of Chr 1, 3 fragments of Chr 3, 8 fragments of Chr 5, 3 fragments of Chr 6, has 2 fragments of Chr 7, 1 fragment of Chr 10, 3 fragments of Chr 11, 2 fragments of Chr 12, 1 fragment of Chr 14, 1 fragment of Chr 16, 1 fragment of Chr 17.

The remaining 94 cell lines contain from 269 (line 25) to 2307 (line 98) positive scores for mouse loci in the current public data set. Note that line 98 contains fragments that represent most of the mouse genome, but that most Chromosomes do have several breakpoints in this cell line.

July 1999. The July posting of RH data includes the 2409 loci of microsatellite markers from the Whitehead/MIT (retrieved June 10 1999).

 
D1Mit59 maps to Chromosome 10, LOD 19.5 to D10Mit109.
D1Mit283 maps to Chromosome 3, LOD 18.9 to D3Mit66.
D1Mit280 maps to Chromosome 3, LOD 6.5 to D3Mit370.
D2Mit507 maps to Chromosome 4, LOD 16 to D4Mit151.
D3Mit205 maps to Chromosome X, LOD 19 to private data in pseudoautosomal region.
D3Mit217 maps to Chromosome 1, LOD 14 to D1Mit325.
D4Mit222 maps to Chromosome 5, LOD 12 to D5Mit378.
D4Mit60 maps to Chromosome 17, LOD 12.2 to D17Mit7.
D4Mit78 maps to Chromosome 12, LOD 12.9 to D12Mit19.
D5Mit379 maps to Chromosome 16, LOD 16.8 to D16Mit84.
D6Mit73 maps to Chromosome 1, LOD 23.2 to D1Mit322.
D6Mit109 maps to Chromosome 11, LOD 16.2 to D11Mit325.
D7Mit215 maps to Chromosome 6, LOD 12 to D6Mit152.
D7Mit221 maps to Chromosome 2, LOD 19.3 to D2Mit94.
D8Mit46 maps to Chromosome 9, LOD 15 to D9Mit118.
D8Mit181 maps to Chromosome 5, LOD 20.3 to D5Mit376.
D8Mit351 maps to Chromosome 10, LOD 17.8 to D10Mit166.
D9Mit199 maps to Chromosome 8, LOD 21.9 to D8Mit152.
D10Mit81 maps to Chromosome 11, LOD 17.7 to D11Mit358.
D10Mit82 maps to Chromosome 13, LOD 19.6 to D13Mit278.
D10Mit278 maps to Chromosome 15, LOD 13.9 to D15Mit13.
D12Mit63 maps to Chromosome 1, LOD 22.6 to D1Mit431.
D12Mit93 maps to Chromosome 17, LOD 14.7 to D17Mit93.
D13Mit40 maps to Chromosome 2, LOD 18.2 to D2Mit261.
D13Mit127 maps to Chromosome 8, LOD 13.3 to D8Mit359.
D14Mit90 maps to Chromosome 2, LOD 16.5 to D2Mit84.
D14Mit169 maps to Chromosome 9, LOD 16 to D9Mit266.
D16Mit118 maps to Chromosome 7, LOD 5 to D7Mit330.
D17Mit163 maps to Chromosome 4, LOD 15.7 to D4Mit289.
D19Mit72 maps to Chromosome 1, LOD 14.9 to D1Mit229.
D19Mit91 maps to Chromosome 10, LOD 20.8 to D10Mit322.
DXMit215 maps to Chromosome 4, LOD 21.6 to D4Mit238.

D6Mit224 maps to Chromosome 6, maps more distally than expected, LOD 18.9 to D6Mit244.
D6Mit355 maps to Chromosome 6, maps more proximally than expected, LOD 20 to D6Mit184.
D8Mit201 maps to Chromosome 8, maps more distally than expected, LOD 15 to D8Mit55.
D8Mit204 maps to Chromosome 8, maps more proximally than expected, LOD 24.5 to D8Mit293.