Guoying Liu

This functional magnetic resonance imaging study investigated the impact of early auditory deprivation and/or use of a visuospatial language [American sign language (ASL)] on the organization of neural systems important in visual motion processing by comparing hearing controls with deaf and hearing native signers. Participants monitored moving flowfields under different conditions of spatial and featural attention. Recruitment of the motion-selective area MT-MST in hearing controls was observed to be greater when attention was directed centrally and when the task was to detect motion features, confirming previous reports that the motion network is selectively modulated by different aspects of attention. More importantly, we observed marked differences in the recruitment of motion-related areas as a function of early experience. First, the lateralization of MT-MST was found to shift toward the left hemisphere in early signers, suggesting that early exposure to ASL leads to a greater reliance on the left MT-MST. Second, whereas the two hearing populations displayed more MT-MST activation under central than peripheral attention, the opposite pattern was observed in deaf signers, indicating enhanced recruitment of MT-MST during peripheral attention after early deafness. Third, deaf signers, but neither of the hearing populations, displayed increased activation of the posterior parietal cortex, supporting the view that parietal functions are modified after early auditory deprivation. Finally, only in deaf signers did attention to motion result in enhanced recruitment of the posterior superior temporal sulcus, establishing for the first time in humans that this polymodal area is modified after early sensory deprivation. Together these results highlight the functional and regional specificity of neuroplasticity in humans.

The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized to investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome. The resulting reduction in genome complexity enables allele-specific hybridization to the array. The selection of SNPs was primarily determined by computer-predicted lengths of restriction fragments containing the SNPs, and was further driven by strict empirical measurements of accuracy, reproducibility, and average call rate, which we estimate to be >99.5%, >99.9%, and>95%, respectively [corrected]. With average heterozygosity of 0.38 and genome scan resolution of 0.31 cM, the SNP array is a viable alternative to panels of microsatellites (STRs). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers.

Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous microarray-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs). Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA), to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM) and mismatch (MM) probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH) without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number estimations using a single array provides additional insight into the structure of genomic alterations. With mean and median inter-SNP euchromatin distances of 244 kilobases (kb) and 119 kb, respectively, this method affords a resolution that is not easily achievable with non-oligonucleotide-based experimental approaches.