TY  - JOUR
AB  - Genome-wide association (GWA) studies are currently one of the most powerful tools in identifying disease-associated genes or variants. In typical GWA studies, single-nucleotide polymorphisms (SNPs) are often used as genetic makers. Therefore, it is critical to estimate the percentage of genetic variations which can be covered by SNPs through linkage disequilibrium (LD). In this study, we use the concept of haplotype blocks to evaluate the coverage of five SNP sets including the HapMap and four commercial arrays, for every exon in the human genome. We show that although some Chips can reach similar coverage as the HapMap, only about 50% of exons are completely covered by haplotype blocks of HapMap SNPs. We suggest further high-resolution genotyping methods are required, to provide adequate genome-wide power for identifying variants.
AU  - Dong, X.*
AU  - Zhong, T.Y.*
AU  - Xu, T.
AU  - Xia, Y.T.*
AU  - Li, B.Q.*
AU  - Li, C.*
AU  - Yuan, L.Y.*
AU  - Ding, G.H.*
AU  - Li, Y.X.*
C1  - 23395
C2  - 31022
SP  - 20-23
TI  - Evaluating coverage of exons by HapMap SNPs.
JO  - Genomics
VL  - 101
IS  - 1
PB  - Elsevier
PY  - 2013
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Pfeiffer, F.*
AU  - Schuster, S.C.*
AU  - Broicher, A.*
AU  - Falb, M.*
AU  - Palm, P.*
AU  - Rodewald, K.*
AU  - Ruepp, A.
AU  - Soppa, J.*
AU  - Tittor, J.*
AU  - Oesterhelt, D.*
C1  - 3765
C2  - 25518
SP  - 553-554
TI  - Genome sequences of Halobacterium salinarum: A reply.
JO  - Genomics
VL  - 91
IS  - 6
PB  - Elsevier
PY  - 2008
SN  - 0888-7543
ER  - 

TY  - JOUR
AB  - We report the sequence of the Halobacterium salinarum strain R1 chromosome and its four megaplasmids. Our set of protein-coding genes is supported by extensive proteomic and sequence homology data. The structures of the plasmids, which show three large-scale duplications (adding up to 100 kb), were unequivocally confirmed by cosmid analysis. The chromosome of strain R1 is completely colinear and virtually identical to that of strain NRC-1. Correlation of the plasmid sequences revealed 210 kb of sequence that occurs only in strain R1. The remaining 350 kb shows virtual sequence identity in the two strains. Nevertheless, the number and overall structure of the plasmids are largely incompatible. Also, 20% of the protein sequences differ despite the near identity at the DNA sequence level. Finally, we report genome-wide mobility data for insertion sequences from which we conclude that strains R1 and NRC-1 originate from the same natural isolate. This exemplifies evolution in the laboratory.
AU  - Pfeiffer, F.*
AU  - Schuster, S.C.*
AU  - Broicher, A.*
AU  - Falb, M.*
AU  - Palm, P.*
AU  - Rodewald, K.*
AU  - Ruepp, A.
AU  - Soppa, J.*
AU  - Tittor, J.*
AU  - Oesterhelt, D.*
C1  - 4259
C2  - 25517
SP  - 335-346
TI  - Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1.
JO  - Genomics
VL  - 91
IS  - 4
PB  - Elsevier
PY  - 2008
SN  - 0888-7543
ER  - 

TY  - JOUR
AB  - No3 (nuclear opacity 3) is a novel congenital nuclear cataract in mice. Microsatellite mapping placed the No3 locus on chromosome 1 between D1Mit480 (32cM) and D1Mit7 (41cM), a region containing seven crystallin genes; Cryba2 and the Cryga-Crygf cluster. Although polymorphic variants were observed, no candidate mutations were found for six of the genes. However, DNA walking identified a murine endogenous retrovirus (IAPLTR1: ERVK) insertion in exon 3 of Cryge, disrupting the coding sequence for gammaE-crystallin. Recombinant protein for the mutant gammaE was completely insoluble. The No3 cataract is mild compared with the effects of similar mutations of gammaE. Quantitative RT-PCR showed that gammaE/F mRNA levels are reduced in No3, suggesting that the relatively mild phenotype results from suppression of gammaE levels due to ERVK insertion. However, the severity of cataract is also strain dependent suggesting that genetic background modifiers also play a role in the development of opacity.
AU  - Nag, N.*
AU  - Peterson, K.*
AU  - Wyatt, K.*
AU  - Hess, S.*
AU  - Ray, S.*
AU  - Favor, J.
AU  - Bogani, D.*
AU  - Lyon, M.*
AU  - Wistow, G.*
C1  - 4165
C2  - 24785
SP  - 512-520
TI  - Endogenous retroviral insertion in Cryge in the mouse No3 cataract mutant.
JO  - Genomics
VL  - 89
IS  - 4
PB  - Elsevier
PY  - 2007
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Zebhauser, R.*
AU  - Kammerer, R.
AU  - Eisenried, A.*
AU  - McLellan, A.*
AU  - Moore, T.*
AU  - Zimmermann, W.*
C1  - 3363
C2  - 23307
SP  - 566-580
TI  - Identification of a novel group of evolutionarily conserved members within the rapidly diverging murine Cea family.
JO  - Genomics
VL  - 86
PY  - 2005
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Hahn, H.*
AU  - Nitzki, F.*
AU  - Schorban, T.*
AU  - Hemmerlein, B.*
AU  - Threadgill, D.*
AU  - Rosemann, M.
C1  - 3220
C2  - 22038
SP  - 853-858
TI  - Genetic mapping of a Ptch1-associated rhabdomyosarcoma susceptibility locus on mouse chromosome 2.
JO  - Genomics
VL  - 84
PY  - 2004
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Hansdottir, A.G.*
AU  - Palsdottier, K.*
AU  - Favor, J.
AU  - Neuhäuser-Klaus, A.
AU  - Fuchs, H.
AU  - Hrabě de Angelis, M.
AU  - Steingrimsson, E.*
C1  - 3886
C2  - 21969
SP  - 932-935
TI  - The novel mouse microphthalmia mutations Mitfmi-enu5 and Mitfmi-bcc2 produce dominant negative Mitf proteins.
JO  - Genomics
VL  - 83
PY  - 2004
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Huang, K.M.*
AU  - Geunes-Boyer, S.*
AU  - Wu, S.*
AU  - Dutra, A.*
AU  - Favor, J.
AU  - Stambolian, D.*
C1  - 3177
C2  - 22166
SP  - 893-901
TI  - Organization and annotation of the Xcat critical region: Elimination of seven positional candidate genes.
JO  - Genomics
VL  - 83
PY  - 2004
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Ihalmo, P.*
AU  - Rinta-Valkama, J.*
AU  - Mai, P.*
AU  - Äström, E.*
AU  - Palmen, T.*
AU  - Pham, T.T.
AU  - Floß, T.
AU  - Holthöfer, H.*
C1  - 2543
C2  - 21931
SP  - 1134-1140
TI  - Molecular cloning and characterization of an endogenous antisense transcript of Nphs1*.
JO  - Genomics
VL  - 83
PY  - 2004
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Müller, S.*
AU  - Finelli, P.*
AU  - Neusser, M.*
AU  - Wienberg, J.
C1  - 959
C2  - 22001
SP  - 458-467
TI  - The evolutionary history of human chromosome 7.
JO  - Genomics
VL  - 84
PY  - 2004
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Runkel, F.*
AU  - Marquardt, A.*
AU  - Stoeger, C.*
AU  - Kochmann, E.*
AU  - Simon, D.*
AU  - Kohnke, B.*
AU  - Korthaus, D.*
AU  - Wattler, F.*
AU  - Fuchs, H.
AU  - Hrabě de Angelis, M.
AU  - Stumm, G.*
C1  - 4258
C2  - 22146
SP  - 824-835
TI  - The dominant alopecia phenotypes Bareskin, Rex-denuded and recuced coat 2 are caused by mutations in gasdermin 3.
JO  - Genomics
VL  - 84
PY  - 2004
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Wahl, M.
AU  - Shukunami, C.*
AU  - Heinzmann, U.
AU  - Hamajima, K.*
AU  - Hiraki, Y.*
AU  - Imai, K.
C1  - 3366
C2  - 22320
SP  - 45-58
TI  - Transcriptome analysis of early chondrogenesis in ATDC5 cells induced by bone morphogenetic protein 4.
JO  - Genomics
VL  - 83
PY  - 2004
SN  - 0888-7543
ER  - 

TY  - JOUR
AB  - We apply a high-throughput protocol of chip-based mass spectrometry (matrix-assisted laser desorption/ionization time-of-flight; MALDI-TOF) as a method of screening for differences in single-nucleotide polymorphism (SNP) allele frequencies. Using pooled DNA from individuals with asthma, Crohn's disease (CD), schizophrenia, type 1 diabetes (T1D), and controls, we selected 534 SNPs from an initial set of 1435 SNPs spanning a 25-Mb region on chromosome 6p21. The standard deviations of measurements of time of flight at different dots, from different PCRs, and from different pools indicate reliable results on each analysis step. In 90% of the disease-control comparisons we found allelic differences of <10%. Of the T1D samples, which served as a positive control, 10 SNPs with significant differences were observed after taking into account multiple testing. Of these 10 SNPs, 5 are located between DQB1 and DRB1, confirming the known association with the DR3 and DR4 haplotypes whereas two additional SNPs also reproduced known associations of T1D with DOB and LTA. In the CD pool also, two earlier described associations were found with SNPs close to DRB1 and MICA. Additional associations were found in the schizophrenia and asthma pools. They should be confirmed in individual samples or can be used to develop further quality criteria for accepting true differences between pools. The determination of SNP allele frequencies in pooled DNA appears to be of value in assigning further genotyping priorities also in large linkage regions.
AU  - Herbon, N.
AU  - Werner, M.
AU  - Braig, C.
AU  - Gohlke, H.
AU  - Dütsch, G.
AU  - Illig, T.
AU  - Altmüller, J.
AU  - Hampe, J.*
AU  - Lantermann, A.*
AU  - Schreiber, S.*
AU  - Bonifacio, E.*
AU  - Ziegler, A.-G.*
AU  - Schwab, S.*
AU  - Wildenauer, D.*
AU  - van den Boom, D.*
AU  - Braun, A.*
AU  - Knapp, M.*
AU  - Reitmeir, P.
AU  - Wjst, M.
C1  - 24008
C2  - 31376
SP  - 510-518
TI  - High-resolution SNP scan of chromosome 6p21 in pooled samples from patients with complex diseases.
JO  - Genomics
VL  - 81
IS  - 5
PB  - Academic Press Inc. Elsevier
PY  - 2003
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Berti, L.
AU  - Mittler, G.
AU  - Przemeck, G.K.H.
AU  - Stelzer, G.
AU  - Günzler, B.
AU  - Amati, F.*
AU  - Conti, E.*
AU  - Dallapiccola, B.*
AU  - Hrabě de Angelis, M.
AU  - Novelli, G.*
AU  - Meisterernst, M.
C1  - 10157
C2  - 21119
SP  - 320-332
TI  - Isolation and Characterization of a Novel Gene from the DiGeorge Chromosomal Region That Encodes for a Mediator Subunit.
JO  - Genomics
VL  - 74
PY  - 2001
SN  - 0888-7543
ER  - 

TY  - JOUR
AB  - The human genome harbors thousands of long terminal repeats (LTRs) that are derived from endogenous retroviruses and contain elements able to regulate the expression of neighboring cellular genes. We have investigated the ability of human endogenous retroviral (HERV)-K LTRs to provide transcriptional processing signals for nonviral sequences. Four chimeric cDNA clones isolated from a cDNA library derived from the human cell line T47D were found to be polyadenylated within an HERV-K-T47D-related LTR. Two transcripts containing an as yet unknown cellular sequence were probably derived from the same genomic locus but their 3' ends were processed at different positions of the LTR. Structural analysis of the polyadenylation site suggests RNA stem-loop structures similar to the HTLV-1 Rex responsive element that bring the two remote AAUAAA and GU-rich elements into the spatial juxtaposition necessary for correct 3' end processing. The cellular part of the third chimeric clone shows significant homology to an exon of the human tyrosine phosphatase 1 gene, although oriented in the antisense direction compared to the adjacent LTR. Furthermore, we found that the 3' untranslated region of the human transmembrane tyrosine kinase gene FLT4 is probably derived from a partial HERV-K-T47D LTR sequence. Taken together, our data suggest that LTRs of the HERV-K-T47D family display biological function by mediating polyadenylation of cellular sequences.
AU  - Baust, C.*
AU  - Seifarth, W.*
AU  - Germaier, H.
AU  - Hehlmann, R.*
AU  - Leib-Mösch, C.
C1  - 21379
C2  - 19495
SP  - 98-103
TI  - HERV-K-T47D-Related Long Terminal Repeats Mediate Polyadenylation of Cellular Transcripts.
JO  - Genomics
VL  - 66
IS  - 1
PY  - 2000
SN  - 0888-7543
ER  - 

TY  - JOUR
AB  - During the mouse ENU mutagenesis screen, mice were tested for the occurrence of dominant cataracts. One particular mutant was discovered as a progressive opacity (Po). Heterozygotes show opacification of a superficial layer of the fetal nucleus, which progresses and finally forms a nuclear opacity. Since the homozygotes have already developed the total cataract at eye opening, the mode of inheritance is semidominant. Linkage analysis was performed using a set of genome-wide microsatellite markers. The mutation was mapped to chromosome 11 distal of the marker D11Mit242 (9.3 ± 4.4 cM) and proximal to D11Mit36 (2.3 ± 2.3 cM). This position makes the βA3/A1-crystallin encoding gene Cryba1 an excellent candidate gene. Mouse Cryba1 was amplified from lens mRNA. Sequence analysis revealed a mutation of a T to an A at the second base of exon 6, leading to an exchange of Trp by Arg. Computer analysis predicts that the fourth Greek key motif of the affected βA3/A1-crystallin will not be formed. Moreover, the mutation leads also to an additional splicing signal, to the skipping of the first 3 bp of exon 6, and finally to the deletion of the Trp residue. Both types of mRNA are present in the homozygous mutant lenses. The mutation will be referred to as Cryba1po1. This particular mouse mutation provides an excellent animal model for a human congenital zonular cataract with suture opacities, which is caused by a mutation in the homologous gene.
AU  - Graw, J.
AU  - Jung, M.*
AU  - Löster, J.
AU  - Klopp, N.
AU  - Soewarto, D.
AU  - Fella, C.
AU  - Fuchs, H.
AU  - Reis, A.*
AU  - Wolf, E.*
AU  - Balling, R.
AU  - Hrabě de Angelis, M.
C1  - 10155
C2  - 21344
SP  - 67-73
TI  - Mutation in the ßA3/A1-Crystallin Encoding Gene Cryba1 Causes a Dominant Cataract in the Mouse.
JO  - Genomics
VL  - 62
PY  - 1999
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Wjst, M.
AU  - Immervoll, T.
AU  - Fischer, G.
AU  - Ulbrecht, M.*
AU  - Gmolka, M.*
AU  - Jung, M.*
AU  - Saar, K.*
AU  - Wichmann, H.-E.
C1  - 20911
C2  - 18956
SP  - 1-8
TI  - A genome-wide search for linkage to asthma.
JO  - Genomics
VL  - 58
PY  - 1999
SN  - 0888-7543
ER  - 

TY  - JOUR
AB  - The human genome contains a family of endogenous retroviruses, HERV-K, with sequence homology to the B-type mouse mammary tumor virus. We have now identified a single HERV-K LTR within the C-type-related human retroviral element S71. The HERV-K LTR is located in the antisense direction between the S71 gag and the pol gene, replacing the 5' half of S71 pol. A number of HERV- K LTR-related cDNA clones were detected by screening various human cDNA libraries with an S71 HERV-K LTR probe, indicating abundant transcription of HERV-K-related LTRs in human tissues. Sequence analysis of four cDNA clones revealed LTR sequences with a nucleotide identity of 70 to 90% with HERV-K10 LTR. Some HERV-K-related LTR sequences contain potential short open reading frames. The analyzed cDNA clones do not harbor any retroviral sequences other than those related to HERV-K LTRs. However, most of the solitary LTRs were found to be coexpressed with cellular sequences. Transcription of these LTRs is probably directed by external cellular promoters. We show that HERV-K LTR- like sequences entered the primate genome about 33-40 million years ago. We estimate the human genome to contain about 25,000 copies of HERV-K-related LTRs, which are distributed over most human chromosomes in an irregular manner.
AU  - Leib-Mösch, C.
AU  - Haltmeier, M.
AU  - Werner, T.
AU  - Geigl, E.M.
AU  - Brack-Werner, R.
AU  - Francke., U.
AU  - Erfle, V.F.
AU  - Hehlmann., R.
C1  - 40324
C2  - 38007
SP  - 261-269
TI  - Genomic distribution and transcription of solitary HERV-K LTRs.
JO  - Genomics
VL  - 18
IS  - 2
PY  - 1993
SN  - 0888-7543
ER  - 

TY  - JOUR
AU  - Morris, D.J.
AU  - Adler, I.-D.
AU  - Robinson, T.J.
C1  - 19824
C2  - 12973
SP  - 323-331
TI  - Somatic Cell Hybrid Mapping on Mouse Chromosome 11 (MMU11): Assignment of 21 Markers Relative to two Breakpoints in band D.
JO  - Genomics
VL  - 15
PY  - 1993
SN  - 0888-7543
ER  - 

TY  - JOUR
AB  - A new family of human endogenous retroviral sequences was recently discovered by way of its relationship to the simian sarcoma-associated virus (SSAV). One molecular clone, termed S71, contains sequences related to the genes coding for the group-specific antigens (gag) and polymerase (pol) proteins of SSAV. At the 3′ end of this human retroviral element we have now found a 535-bp region which shows features characteristic of a retroviral long terminal repeat, including potential signal sequences essential for transcriptional control. By means of Southern blotting and in situ hybridization, the sequence was mapped to chromosome 18 band q21.
AU  - Brack-Werner, R.
AU  - Barton, D.E.
AU  - Werner, T.*
AU  - Foellmer, B.E.
AU  - Leib-Mösch, C.*
AU  - Francke., U.
AU  - Erfle, V.F.
AU  - Hehlmann., R.*
C1  - 41217
C2  - 36514
SP  - 68-75
TI  - Human SSAV-related endogenous retroviral element: LTR-like sequence and chromosomal localization to 18q21.
JO  - Genomics
VL  - 4
IS  - 1
PY  - 1989
SN  - 0888-7543
ER  -