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Status report on gap closure of the human chromosome 5 BAC map

Status report on gap closure of the human chromosome 5 BAC map. Authentication of C5 BAC maps Map and sequence status Gap status and steps used to close gaps Status of the centromere and telomeres C5 specific duplications. Jan-Fang Cheng Joint Genome Institute. May 24, 2001.

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Status report on gap closure of the human chromosome 5 BAC map

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  1. Status report on gap closure of the human chromosome 5 BAC map • Authentication of C5 BAC maps • Map and sequence status • Gap status and steps used to close gaps • Status of the centromere and telomeres • C5 specific duplications Jan-Fang Cheng Joint Genome Institute May 24, 2001

  2. Authentication of C5 BAC contigs • Restriction fragment overlaps • Sequence overlaps • FISH data • UniSTS matches • BAC end matches • FPC map

  3. C5 map and sequence status • Size of chromosome 5: ~200 Mb • Coverage of restriction mapped clones: 184,306 Kb • Number of JGI committed clones: 1989 • Coverage of committed clones: 172,083 Kb • Size of JGI sequenced clones: 141,027 Kb • Marked clones: 1,912 Kb • Drafted clones: 77,356 Kb • Finished clones: 61,759 Kb • Feb. 10 release of the Golden Path: 165 Mb of sequence and 35 Mb of gap

  4. How many Type 2: Gaps with FPC bridging clones FPC 95 Restriction map + FISH Type 3: Gaps with no bridging clones Celera Scaffold 11 STS + Restriction map + FISH 22 (STS + Restriction map + FISH) n Gap status and steps used to close gaps

  5. ? Kb p YAC BAC RP11-811I15 927 Kb RP11-236F16 600 Kb BAC BAC q 8.26 Mb YAC RP1-9H3 RP11-324K20 400 Kb CTD-2276O24 120 Kb Map status of C5 centromere and telomeres

  6. Mapping of tandemly duplicated gene:Protocadherin gene cluster on 5q31 Wu et al., (2001) Genome Research 11: 389-404

  7. p q C5 specific duplications RP11-374A4 RP11-96B3 RP11-360I2 597 Kb (6 BACs) NAIP SMN 500 Kb RP11-430F16 RP11-356O21 ?? SMN NAIP 500 Kb 15 Mb CTD-2021M10 RP11-3M7

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