Biology Reference
In-Depth Information
either on research websites or on public database websites. See
Box 16.2
for a list of some of
the more popularly used database sites.
Generating DNA data can also be straightforward, particularly if you are dealing with
DNA that has not yet decayed substantially. Regardless of DNA quality, basic and standard-
ized methods exist for retrieving it. These are summarized below in four steps and in
Figure 16.4
.
STEP 1: SAMPLE PREPARATION
If your DNA source is bone or teeth, your sample will need to be prepared for DNA extrac-
tion by first decontaminating the sample of exogenous DNA (i.e. that not from the indi-
vidual). This involves removing exposed surfaces followed by successive washes in
BOX 16.2
COMMONLY USED PUBLIC DNA DATABASES
National Center for Biotechnology
Information (NCBI) Databases
: Provides
a more-or-less comprehensive listing of major
databases, including references, nucleotide
and protein sequences, protein structures,
dbGaP
: The database of Genotypes and
Phenotypes (dbGaP) was developed to
archive and distribute the results of studies
that have investigated the interaction of
genotype and phenotype.
Access
:
http://www.ncbi.nlm.nih.gov/gap
GenBank
: National Institutes of Health
(NIH) genetic sequence database, an anno-
tated collection of all publicly available DNA
SPSmart
: This is a reprocessing engine for
any given population-based genotype data-
base that is able to deal even with billions of
genotypes, and that is also capable of
summarizing all that information into the
most common population genetics indices.
Access
:
http://spsmart.cesga.es
The Genographic Project Public Partici-
pation Mitochondrial DNA Database
:The
Genographic Project is studying the genetic
signatures of ancient human migrations and
creating an open-source research database. It
allows members of the public to participate in
a real-time anthropological genetics study by
submitting personal samples for analysis and
donating the genetic results to the database. The
first 18 months of public participation in the
Genographic Project can be currently accessed
as the largest standardized human mitochon-
drial DNA (mtDNA) database ever collected,
Y Chromosome Haplotype Reference
Database (YHRD)
: A free searchable Y-STR
9
Behar, D.M., Rosset, S., Blue-Smith, J., Balanovsky,
O., Tzur, S., Comas, D., Mitchell, R.J., Quintana-
Murci, L., Tyler-Smith, C., Wells, R.S., Genographic
Consortium. The Genographic Project public partici-
pation mitochondrial DNA database. PLoS Genetics
2007, 3(6), e104.
