A BAC clone fingerprinting approach to the detection of human genome rearrangements

Krzywinski, Martin; Bosdet, Ian; Mathewson, Carrie; Wye, Natasja; Brebner, Jay; Chiu, Readman; Corbett, Richard; Field, Matthew; Lee, Darlene; Pugh, Trevor; Volik, Stas; Siddiqui, Asim; Jones, Steven; Schein, Jacquie; Collins, Collin; Marra, Marco

doi:10.1186/gb-2007-8-10-r224

Table 5 PCR primers used to validate the presence of breakpoints detected by fingerprints

From: A BAC clone fingerprinting approach to the detection of human genome rearrangements

	Left primer				Right primer
Primer transform	Sequence		Position		Sequence		Position
		Chr	Start (bp)	End (bp)		Chr	Start (bp)	End (bp)
M0092D11
ar+ br+	TGCTAAATTTCCCAAGTGCC	20	45,794,352	45,794,371	CCGTCCTCTTAGCGAACTTG	20	46,968,304	46,968,323
ar+ br-	TGCTAAATTTCCCAAGTGCC	20	45,794,352	45,794,371	AATTTCAAAATGCGTCTGGG	20	46,968,631	46,968,650
ar+ bl+	TGCTAAATTTCCCAAGTGCC	20	45,794,352	45,794,371	TGACACGCAGGGTAGATCAG	20	46,923,060	46,923,079
ar+ bl-	TGCTAAATTTCCCAAGTGCC	20	45,794,352	45,794,371	TCCAACAGGAAGGAGTACCG	20	46,922,743	46,922,762
al+ br+	CTCTCTTTTGTGGGACGAGC	20	45,718,752	45,718,771	CCGTCCTCTTAGCGAACTTG	20	46,968,304	46,968,323
al+ br-	CTCTCTTTTGTGGGACGAGC	20	45,718,752	45,718,771	AATTTCAAAATGCGTCTGGG	20	46,968,631	46,968,650
al+ bl+	CTCTCTTTTGTGGGACGAGC	20	45,718,752	45,718,771	TGACACGCAGGGTAGATCAG	20	46,923,060	46,923,079
al+ bl-	CTCTCTTTTGTGGGACGAGC	20	45,718,752	45,718,771	TCCAACAGGAAGGAGTACCG	20	46,922,743	46,922,762
M0107O02
br+ ar+	AATAGAAGCCAGGCATGGTG	20	48,861,156	48,861,175	GTTAGGAGGAGGGTGGAACC	17	56,663,181	56,663,200
br+ ar-	AATAGAAGCCAGGCATGGTG	20	48,861,156	48,861,175	TAGCCGTTCTGACTGGTGTG	17	56,663,261	56,663,280
br+ al+	AATAGAAGCCAGGCATGGTG	20	48,861,156	48,861,175	TAGCTGGGATTACAGGTGCC	17	56,646,379	56,646,398
br+ al-	AATAGAAGCCAGGCATGGTG	20	48,861,156	48,861,175	ACAACCTGTCCGACCAGAAC	17	56,646,305	56,646,324
M0141F19
ar+ cr+	GGACAGAGGCTTTTGTAGCG	17	56,687,628	56,687,647	ACCACGTAGACAAAGACGGG	20	59,173,964	59,173,983
ar+ cr-	GGACAGAGGCTTTTGTAGCG	17	56,687,628	56,687,647	TTCTGGATTCTCCTTGGTGC	20	59,173,950	59,173,969
ar+ cl+	GGACAGAGGCTTTTGTAGCG	17	56,687,628	56,687,647	ATTTGGTTCCTGGTGAGTGC	20	59,153,746	59,153,765
ar+ cl-	GGACAGAGGCTTTTGTAGCG	17	56,687,628	56,687,647	AGAAGAACCCGACGACATTG	20	59,153,849	59,153,868
br+ cr+	TATCCTTCAGGAATCGCCAC	20	53,542,992	53,543,011	ACCACGTAGACAAAGACGGG	20	59,173,964	59,173,983
br+ cr-	TATCCTTCAGGAATCGCCAC	20	53,542,992	53,543,011	TTCTGGATTCTCCTTGGTGC	20	59,173,950	59,173,969
br+ cl+	TATCCTTCAGGAATCGCCAC	20	53,542,992	53,543,011	ATTTGGTTCCTGGTGAGTGC	20	59,153,746	59,153,765
br+ cl-	TATCCTTCAGGAATCGCCAC	20	53,542,992	53,543,011	AGAAGAACCCGACGACATTG	20	59,153,849	59,153,868

Primer sequence is the appropriately transformed (reversed, complemented, reverse-complemented) primer sequence to test a specific order/orientation of clone regions within the insert. Products were detected for reactions where the primer transform field is in bold. Primer combinations (e.g. ar+ br+) correspond to order and orientation of putative rearrangement and are described in detail in Additional data file 1.

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ISSN: 1474-760X

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