McLay KE

References (3)

Title : The DNA sequence and biological annotation of human chromosome 1 - Gregory_2006_Nature_441_315
Author(s) : Gregory SG , Barlow KF , McLay KE , Kaul R , Swarbreck D , Dunham A , Scott CE , Howe KL , Woodfine K , Spencer CC , Jones MC , Gillson C , Searle S , Zhou Y , Kokocinski F , McDonald L , Evans R , Phillips K , Atkinson A , Cooper R , Jones C , Hall RE , Andrews TD , Lloyd C , Ainscough R , Almeida JP , Ambrose KD , Anderson F , Andrew RW , Ashwell RI , Aubin K , Babbage AK , Bagguley CL , Bailey J , Beasley H , Bethel G , Bird CP , Bray-Allen S , Brown JY , Brown AJ , Buckley D , Burton J , Bye J , Carder C , Chapman JC , Clark SY , Clarke G , Clee C , Cobley V , Collier RE , Corby N , Coville GJ , Davies J , Deadman R , Dunn M , Earthrowl M , Ellington AG , Errington H , Frankish A , Frankland J , French L , Garner P , Garnett J , Gay L , Ghori MR , Gibson R , Gilby LM , Gillett W , Glithero RJ , Grafham DV , Griffiths C , Griffiths-Jones S , Grocock R , Hammond S , Harrison ES , Hart E , Haugen E , Heath PD , Holmes S , Holt K , Howden PJ , Hunt AR , Hunt SE , Hunter G , Isherwood J , James R , Johnson C , Johnson D , Joy A , Kay M , Kershaw JK , Kibukawa M , Kimberley AM , King A , Knights AJ , Lad H , Laird G , Lawlor S , Leongamornlert DA , Lloyd DM , Loveland J , Lovell J , Lush MJ , Lyne R , Martin S , Mashreghi-Mohammadi M , Matthews L , Matthews NS , Mclaren S , Milne S , Mistry S , Moore MJ , Nickerson T , O'Dell CN , Oliver K , Palmeiri A , Palmer SA , Parker A , Patel D , Pearce AV , Peck AI , Pelan S , Phelps K , Phillimore BJ , Plumb R , Rajan J , Raymond C , Rouse G , Saenphimmachak C , Sehra HK , Sheridan E , Shownkeen R , Sims S , Skuce CD , Smith M , Steward C , Subramanian S , Sycamore N , Tracey A , Tromans A , Van Helmond Z , Wall M , Wallis JM , White S , Whitehead SL , Wilkinson JE , Willey DL , Williams H , Wilming L , Wray PW , Wu Z , Coulson A , Vaudin M , Sulston JE , Durbin R , Hubbard T , Wooster R , Dunham I , Carter NP , McVean G , Ross MT , Harrow J , Olson MV , Beck S , Rogers J , Bentley DR , Banerjee R , Bryant SP , Burford DC , Burrill WD , Clegg SM , Dhami P , Dovey O , Faulkner LM , Gribble SM , Langford CF , Pandian RD , Porter KM , Prigmore E
Ref : Nature , 441 :315 , 2006
Abstract : The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.
ESTHER : Gregory_2006_Nature_441_315
PubMedSearch : Gregory_2006_Nature_441_315
PubMedID: 16710414
Gene_locus related to this paper: human-LYPLAL1 , human-PPT1 , human-TMCO4 , human-TMEM53

Title : DNA sequence and analysis of human chromosome 9 - Humphray_2004_Nature_429_369
Author(s) : Humphray SJ , Oliver K , Hunt AR , Plumb RW , Loveland JE , Howe KL , Andrews TD , Searle S , Hunt SE , Scott CE , Jones MC , Ainscough R , Almeida JP , Ambrose KD , Ashwell RI , Babbage AK , Babbage S , Bagguley CL , Bailey J , Banerjee R , Barker DJ , Barlow KF , Bates K , Beasley H , Beasley O , Bird CP , Bray-Allen S , Brown AJ , Brown JY , Burford D , Burrill W , Burton J , Carder C , Carter NP , Chapman JC , Chen Y , Clarke G , Clark SY , Clee CM , Clegg S , Collier RE , Corby N , Crosier M , Cummings AT , Davies J , Dhami P , Dunn M , Dutta I , Dyer LW , Earthrowl ME , Faulkner L , Fleming CJ , Frankish A , Frankland JA , French L , Fricker DG , Garner P , Garnett J , Ghori J , Gilbert JG , Glison C , Grafham DV , Gribble S , Griffiths C , Griffiths-Jones S , Grocock R , Guy J , Hall RE , Hammond S , Harley JL , Harrison ES , Hart EA , Heath PD , Henderson CD , Hopkins BL , Howard PJ , Howden PJ , Huckle E , Johnson C , Johnson D , Joy AA , Kay M , Keenan S , Kershaw JK , Kimberley AM , King A , Knights A , Laird GK , Langford C , Lawlor S , Leongamornlert DA , Leversha M , Lloyd C , Lloyd DM , Lovell J , Martin S , Mashreghi-Mohammadi M , Matthews L , Mclaren S , McLay KE , McMurray A , Milne S , Nickerson T , Nisbett J , Nordsiek G , Pearce AV , Peck AI , Porter KM , Pandian R , Pelan S , Phillimore B , Povey S , Ramsey Y , Rand V , Scharfe M , Sehra HK , Shownkeen R , Sims SK , Skuce CD , Smith M , Steward CA , Swarbreck D , Sycamore N , Tester J , Thorpe A , Tracey A , Tromans A , Thomas DW , Wall M , Wallis JM , West AP , Whitehead SL , Willey DL , Williams SA , Wilming L , Wray PW , Young L , Ashurst JL , Coulson A , Blocker H , Durbin R , Sulston JE , Hubbard T , Jackson MJ , Bentley DR , Beck S , Rogers J , Dunham I
Ref : Nature , 429 :369 , 2004
Abstract : Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.
ESTHER : Humphray_2004_Nature_429_369
PubMedSearch : Humphray_2004_Nature_429_369
PubMedID: 15164053
Gene_locus related to this paper: human-CEL

Title : The DNA sequence and comparative analysis of human chromosome 10 - Deloukas_2004_Nature_429_375
Author(s) : Deloukas P , Earthrowl ME , Grafham DV , Rubenfield M , French L , Steward CA , Sims SK , Jones MC , Searle S , Scott C , Howe K , Hunt SE , Andrews TD , Gilbert JG , Swarbreck D , Ashurst JL , Taylor A , Battles J , Bird CP , Ainscough R , Almeida JP , Ashwell RI , Ambrose KD , Babbage AK , Bagguley CL , Bailey J , Banerjee R , Bates K , Beasley H , Bray-Allen S , Brown AJ , Brown JY , Burford DC , Burrill W , Burton J , Cahill P , Camire D , Carter NP , Chapman JC , Clark SY , Clarke G , Clee CM , Clegg S , Corby N , Coulson A , Dhami P , Dutta I , Dunn M , Faulkner L , Frankish A , Frankland JA , Garner P , Garnett J , Gribble S , Griffiths C , Grocock R , Gustafson E , Hammond S , Harley JL , Hart E , Heath PD , Ho TP , Hopkins B , Horne J , Howden PJ , Huckle E , Hynds C , Johnson C , Johnson D , Kana A , Kay M , Kimberley AM , Kershaw JK , Kokkinaki M , Laird GK , Lawlor S , Lee HM , Leongamornlert DA , Laird G , Lloyd C , Lloyd DM , Loveland J , Lovell J , Mclaren S , McLay KE , McMurray A , Mashreghi-Mohammadi M , Matthews L , Milne S , Nickerson T , Nguyen M , Overton-Larty E , Palmer SA , Pearce AV , Peck AI , Pelan S , Phillimore B , Porter K , Rice CM , Rogosin A , Ross MT , Sarafidou T , Sehra HK , Shownkeen R , Skuce CD , Smith M , Standring L , Sycamore N , Tester J , Thorpe A , Torcasso W , Tracey A , Tromans A , Tsolas J , Wall M , Walsh J , Wang H , Weinstock K , West AP , Willey DL , Whitehead SL , Wilming L , Wray PW , Young L , Chen Y , Lovering RC , Moschonas NK , Siebert R , Fechtel K , Bentley D , Durbin R , Hubbard T , Doucette-Stamm L , Beck S , Smith DR , Rogers J
Ref : Nature , 429 :375 , 2004
Abstract : The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.
ESTHER : Deloukas_2004_Nature_429_375
PubMedSearch : Deloukas_2004_Nature_429_375
PubMedID: 15164054
Gene_locus related to this paper: human-LIPA , human-LIPK , human-PNLIPRP1 , human-PNLIPRP2 , human-PNLIPRP3