For each patient, amplicons containing each exon and adjacent flanking regions of the
TYR,
OCA2 (
P),
TYRP1, and
SLC45A2 (
MATP) genes, the 5′ promoter regions of
TYR (1555 nucleotides [nt], excluding a simple sequence repeat from nt 88549828-88550258) and
OCA2, and a conserved 647-bp segment located 8989 bp upstream from the
TYR major mRNA 5′ terminus that may represent a locus control region,
12 were amplified by touchdown PCR for DNA sequencing. For patients with no apparent pathologic mutations in any of these genes, amplicons containing each exon of the
HPS1,
HPS4, and
SILV genes were then amplified for sequencing (in many patients DNA sequencing of multiple genes was performed in parallel). PCR primers are listed in
Supplementary Table S2. PCRs were performed in 25-μL volumes containing 30 ng DNA, 5 pmols of each primer, 2.5 μL of 10× PCR buffer, 1.5 mM MgCl
2, 1.25 M betaine, 0.2 mM dNTPs (GeneAmp dNTP Blend; Applied Biosystems, Inc. [ABI], Foster City, CA), and 2.0 U
Taq DNA polymerase (Platinum
Taq; Invitrogen). For most amplicons, DNA was denatured at 94°C for 10 minutes followed by 15 cycles of denaturation at 94°C for 30 seconds, annealing from 63°C to 56°C for 45 seconds decreasing 0.5°C each cycle, and elongation at 72°C for 1 minute, followed by an additional 25 cycles of denaturation at 94°C for 30 seconds, annealing at 56°C for 45 seconds, and elongation at 72°C for 1 minute, followed by a final extension at 72°C for 10 minutes in a thermocycler (model 9600 or 9700; ABI). For
TYR exon 4 the annealing range was further decreased to 54°C by adding four more cycles at the initial stage and by decreasing the annealing temperature of the following 25 cycles to 54°C.