Table A3.

High-Resolution Mapping of Proximal and Distal Breakpoints

Patient(s)	ProximalPrimerPairsa	ProximalIntervalLengthb(kb)	DistalPrimerPairsa	DistalIntervalLengthb(kb)	Comments
AMC0110	Table A4	1.5
WHT4396	Table A4	1.8
WHT3935					Both proximal and distal breakpoints are masked
WHT2943	Table A4	See comments	Table A6	2	We initially mistook the small, 2.7-kb deletion in P5 for the P5/distal-P1 deletion but then amplified the deletion junction by using long-range PCR with primers that bracket both the 2.7-kb deletion and the P5/distal-P1 deletion (GenBank accession number AF395669) (table A8)
WHT3410	Table A4	See comments	Table A6	See comments	High-resolution breakpoint mapping was complicated, because spacer orientation in both P5 and P1.1 is reversed compared to the reference sequence (expected to be a common polymorphism); we therefore successfully attempted long-range PCR by using primers in the proximal arm of P5 and the distal arm of P1.1 (table A8)
WHT3516, WHT3642, WHT4426, and WHT4486			Table A6	1.5
AMC0111			Table A6	10	Masking by the distal arm of P1.1 precluded finer localization of distal breakpoint
WHT2825	Table A5	1.2	Table A6	1.0

^aTable that shows primer pairs and PCR results used to refine breakpoint locations.

^bLengths of intervals to which breakpoints were localized by high-resolution breakpoint mapping.