For haplotype analyses in patients, 10 established
microsatellite loci (DXS556, DXS8042, DXS1368, DXS574, DXS993, DXS8012,
DXS1207, DXS1201, DXS8085, and DXS228) located within Xp11.4 were
analyzed. The locus order was confirmed by physical mapping of the
markers to the Xp11 subregional panels and yeast artificial
chromosomes. One of the primers of each pair of oligonucleotides was
fluorescence-labeled at the 5′ terminus with FAM, HEX, or TET. A
touchdown protocol for PCR amplification (GeneAmp 9600 PCR cycler; PE
Biosystems, Foster City, CA) was accomplished with an initial
denaturation of 5 minutes at 94°C; 5 cycles at 94°C for 15 seconds,
60°C for 30 seconds, and 72°C for 30 seconds; 5 cycles at 94°C
for 15 seconds, 57°C for 30 seconds, and 72°C for 30 seconds; and
25 cycles at 94°C for 15 seconds, 52°C for 15 seconds, and 72°C
for 30 seconds; and a final extension at 72°C for 5 minutes. The PCR
products were pooled and an internal length standard (Prism
Genescan-500; PE Biosystems) was added. The pooled products were
separated using 6% denaturing polyacrylamide gels on an automated DNA
sequencer (model ABI 373A, equipped with Genescan software; PE
Biosystems).
The procedure for identifying mutations in the
NYX gene has
been described in detail.
15 Briefly, blood was collected
from patients with CSNB1 and control subjects, and DNA was extracted
from white blood cells according to standard procedures.
28 Five overlapping segments covering the entire
NYX coding
region were amplified by means of polymerase chain reaction (PCR). The
PCR products were purified by agarose gel-extraction (QiaQuick; Qiagen,
Chatsworth, CA), cycle sequenced with dye-terminator chemistry (BigDye;
PE Biosystems), and analyzed on a DNA sequencer (model ABI 377; PE
Biosystems). Cosegregation analysis of mutations and their exclusion in
control subjects was performed by restriction fragment length
polymorphism (RFLP), single-strand conformational polymorphism (SSCP),
Southern hybridization, or direct sequence analysis.