69genotyping, determining the restriction fragment length polymorphisms (RFLPs) is
still one of the most convenient and cost-saving methods. Abnormalities in mito-
chondrial complex I, which is responsible for controlling mitochondrial function,
have been implicated in a variety of diseases associated with mitochondrial dysfunc-
tion including schizophrenia. The NADH dehydrogenase Fe-S protein 1 (NDUFS1)
is the largest subunit of complex I. Findings of a study suggest that NDUFS1 may
confer susceptibility to schizophrenia in male subjects, acting as a causative factor
for the severity of negative symptoms in schizophrenia (Zhu et al. 2014 ).
Limitations of SNP in Genetic Testing
Genotyping for complex diseases may be insuffi cient to predict whether a person is
at risk for a particular disease. One tries to associate SNPs with disease, but if no
SNP in a certain gene predicts disease, further interest in the gene or protein or
enzyme is lost. In some cases, the phenotype expressed by a gene provides a more
accurate risk assessment. Genotypes of the paraoxonase (PON1) gene on chromo-
some 7 are associated with atherosclerosis or cardiovascular disease (CVD) but the
genotype in these subjects does not always refl ect the phenotype of patients with
CVD. These results support the benefi t of a “level crossing” approach that includes
intervening phenotypes in the study of complexly inherited disease. Therefore,
there is a need to look beyond SNP studies to understand genetic contributions to
complex disease.
Another example is the search for a gene for phenylketonuria (PKU), where the
investigators have looked for an association between individual restriction fragment-
length polymorphisms (RFLPs), and PKU mutations. While haplotypes were clearly
associated with disease, individual RFLP sites were not because they will cancel out
if there are many mutations at a locus.
Concluding Remarks on SNP Genotyping
Several methods are available for SNP genotyping. For 10 or fewer SNPs and sam-
ple numbers in the thousands, the current gold standard is TaqMan real-time
PCR. MassARRAY system, a mass spectrometry-based platform, is suitable for
high throughput and up to 1,000 SNPs. Pyrosequencing, a sequencing-by-synthesis
method can be used for up to 100 SNPs. Affymetrix provides the densest coverage
at the whole-genome level with its GeneChip Human Mapping 500 K Array Set and
Affymetrix GeneChip® Scanner 3000 MegAllele, and enables the highest level of
multiplexing that is commercially available as well as increase throughput with low
capital investment. Illumina is supplementing its current 100 K chip with a 250 K
chip. RFLP analysis is laborious and hit-and-miss as success depends on whether
the restriction enzyme recognizes particular SNPs. It is relatively inexpensive,
which makes it appropriate for a small number of SNPs and a small number of
samples. New methods for SNP genotyping are being investigated. The presence of
SNP Genotyping