Cheek Swab Collection and DNA Extraction

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					Cheek Swab Collection and DNA Extraction
Mark Neff, PhD, Veterinary Genetics Laboratory, University of California - Davis
Invited by Eddie Dziuk, Delegate, National Beagle Club
                                                                         HEALTH ISSUES

 R   ecently, the Broad
     Institute of MIT/Harvard
has presented the canine
                                  essary degree of breeder par-
                                    Cheek swabs strike an
                                                                    always recommended). Cheek
                                                                    swab DNA can be arrayed in
                                                                    conventional laboratory plates
genetics community with a         important balance – these         and allowed to dessicate,
whole genome sequence of          samples provide ample DNA of      which facilitates high-
the dog. This is an unprece-      sufficient quality for the most   throughput DNA analysis.
dented advance in the field –     common laboratory method of         There are new technologies
the genome sequence will          DNA fingerprinting. At the        on the horizon for which
enable researchers to transi-     same time, the ease and low       cheek swab DNA may not be a
tion from family-based studies    cost of collecting swabs dra-     suitable substrate (namely,
that identify the determinants    matically lower the barriers to   detecting single base differ-
of simple traits, to more pow-    breeder participation (relative   ences using high density DNA
erful population-based            to blood collections). One or     chips). Most genetic
approaches that can elucidate     more swabs can be obtained        research, however, emphasizes
the genetic components of         from a dog in less than five      the most recent generations
multi-factorial traits (i.e.,     minutes without the need for      of dogs, primarily so that
complex diseases).                a visit to a veterinary clinic.   accurate and standardized
  Mapping genes with popula-      The swabs can then be             methods of phenotyping (i.e.,
tions requires two key            shipped in an envelope by         diagnostics) can be applied
resources. First, digitized       regular post to the laboratory,   during sample ascertainment.
whole-breed genealogies must      where they can be stored at       Older generations of dogs add
be assembled to optimize          room temperature indefinitely.    power to studies, but this is
selection of animals for inclu-   Ongoing studies indicate that     usually to augment or confirm
sion in the study (this allows    swabs can provide DNA for at      a finding. If emergent tech-
researchers to calibrate the      least eight years, so long as     nologies turn out to require
size and intensity of the         ambient humidity is not too       DNA derived from blood sam-
genome signal that they are       high.                             ples, these samples can still
searching for). The AKC has         The DNA extracted from a        be readily collected from
recently made electronic pedi-    single swab is sufficient for     extant dogs. Cheek swab
gree data accessible to aca-      running 200 polymerase chain      samples from older, possibly
demic researchers to facilitate   reactions (PCRs), with as         deceased dogs will still retain
this step. Second, DNA must       many as eight genetic markers     their value and provide the
be collected from a large         per reaction. This marker         needed data for strengthening
number of animals (typically,     density is at the threshold       or confirming genetic associa-
greater than 200 dogs) for        needed for population-based       tions.       D
both the case (affected) and      mapping; multiple swabs can
control (unaffected) groups       be collected per dog to ensure
that make up a population-        that enough genetic material
based project. Cheek swabs        has been collected (roughly
currently represent the best      2% of swabs fail to provide
means for achieving the nec-      DNA, so additional swabs are

                                              PERSPECTIVES                           SEPTEMBER 2005   5

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