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 ChengJoint Genome Institute

May 24, 2001

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Authentication of C5 BAC contigs

• Restriction fragment overlaps

• FISH data

• UniSTS matches

• BAC end matches

• FPC map

• Sequence overlaps

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

Gap status and steps used to close gaps

Restriction map + FISH

STS + Restriction map + FISH

(STS + Restriction map + FISH) n

Type 3: Gaps with no bridging clones

11

Celera Scaffold

22

Type 2: Gaps with FPC bridging clonesFPC

How many

95

Map status of C5 centromere and telomeres

RP11-811I15

? Kb

927 Kb

BAC

BACYAC

RP1-9H3

CTD-2276O24

RP11-236F16

400 Kb

600 Kb

RP11-324K20

120 Kb

8.26 Mb

YAC

BAC

q

p

Mapping of tandemly duplicated gene:Protocadherin gene cluster on 5q31

Wu et al., (2001) Genome Research 11: 389-404

C5 specific duplications

q

pRP11-374A4

RP11-96B3

NAIPSMN

SMNNAIP

500 Kb

500 Kb

597 Kb (6 BACs)

RP11-360I2

15 Mb

RP11-3M7CTD-2021M10

RP11-356O21

RP11-430F16

??