Oligonucleotide Array Comparative Genomic Hybridization (oaCGH) based characterization of genetic deficiencies as an aid to gene mapping in Caenorhabditis elegans

Table 1 Summary of mapping resolution for deficiencies using both genetic and molecular mapping techniques.

				Genetic/PCR Mapping Data		oaCGH Mapping Data		^aSequenced Breakpoint Coordinates
Strain	Deficiency	Mutagen	Position	LEFT Cosmid	RIGHT Cosmid	LEFT (bp)	RIGHT (bp)	LEFT (bp)	RIGHT (bp)	Size of deficiency (kb)
MT3022	nDf20	GRI	Out	egl-5	sma-2	7895240	8678216	7896734	8676211	780
			In	lin-36	dpy-19	7900966	8676164
BC4698	sDf121	GRI	Out	F10G11	C05D2	4568979	5637318	4568042	5637312	1069
			In	F35G12	F54E7	4569058	5636068
BC4634	sDf125	UVI	Out	F42A10	K04C2	6178564	6620842	6178994	6620106	441
			In	C23G10	R13F6	6181034	6619737
BC4638	sDf127	UVI	Out	C23G10	R13A5	6200904	7453868	ND	ND	^d1194–1253
			In	C23G10	T20B12	6200951	7395215
BC4690	sDf128	GRI	Out	C29E4	C06G4	7945153	8023540	7945392	8023387	78
			In	C06G4	F44B9	7945526	8019512
BC4637	sDf130	UV	Out	C32A3	C05D2	3640014	5566628	3640101	5565581	1925
			In			3640119	5565449
			Out			5635618	5664335	ND	ND	^e16–29
			In	R13G10	ZC155	5645065	5661035
BC4677	sDf135	GRI	Out	B0361	T20B12	7276848	7479897	7277386	7476402	199
			In	T20B12	R13A5	7277471	7467958
^bNA	sDp3	GRI	Out	daf-7	dpy-19	^cComplex	8611252	NA	NA	NA
			In	dpy-18	mig-10		8611166
BC3737	sDp8	UVI	Out	let-721	sma-2	6559307	8714234	NA	NA	NA
			In	M01G4	dpy-19	6562088	8710120
Average resolution (kb)				117		5.6		0	0

^aBreakpoint coordinates aligned to Wormbase (release WS170).
^bsDp3 structure is inferred from the background of the oaCGH data.
^cThe left breakpoint of sDp3 is fragmented over a large region.
^dThe right breakpoint of sDf127 falls within a 50 kb region of low complexity and therefore low probe density and could not be accurately defined.
^eThe second deleted region in sDf130 was not be resolved by PCR analysis.

ISSN: 1471-2164