Percentage of samples with high molecular weight DNA (>23 kb) and PCR success rates to amplify fragments of the β-globin gene from phase 1 of the study by method of collection and DNA extraction
Method of collection DNA extraction | N | % samples with high molecular weight DNAa | PCR success rate | ||||
---|---|---|---|---|---|---|---|
268 bp | 536 bp | 989 bpb | |||||
Cytobrushesc | |||||||
Phenol-chloroform | 40 | 55%def | 100%g | 97.5h | 94.4%i | ||
QIAamp kit | 40 | 2.5%dj | 100% | 92.5% | 89.5% | ||
NaOH | 40 | 0.0%e | 40.0%g | 20.0%h | 15.0%i | ||
Mouthwashk | |||||||
Phenol-chloroform | 35 | 94.3%flm | 100% | 100% | 100% | ||
QIAamp kit | 30 | 13.3%jl | 100% | 100% | 100% | ||
Puregene kit | 20 | 100%m | 100% | 100% | 100% |
a High molecular weight DNA was defined as grade 5 on the agarose gel (i.e., DNA fragments >23 kb).
b Respectively, amplification of the 989-bp fragment was not attempted in 4, 21, and 26 cytobrush samples extracted by phenol-chloroform, QIAamp kit, and NaOH due to low sample concentration.
c Each DNA extraction arm includes 40 cytobrush samples from a total of 120 women participating in the WHS (i.e., independent observations in each arm).
d P < 0.001, cytobrush phenol-chloroform versus cytobrush QIAamp kit, Fisher’s exact test.
e P < 0.001, cytobrush phenol-chloroform versus cytobrush NaOH, Fisher’s exact test.
f P < 0.001, cytobrush phenol-chloroform versus mouthwash phenol-chloroform, Fisher’s exact test.
g P < 0.001 cytobrush phenol-chloroform versus cytobrush NaOH, Fisher’s exact test.
h P < 0.001 cytobrush phenol-chloroform versus cytobrush NaOH, Fisher’s exact test.
i P < 0.001 cytobrush phenol-chloroform versus cytobrush NaOH, Fisher’s exact test.
j P = 0.16, cytobrush QIAamp versus mouthwash QIAamp kit, Fisher’s exact test.
k Each DNA extraction arm includes one of three aliquots of equal volume made from single mouthwash samples collected from a total of 40 men participating in the AHS (i.e., paired observations in each arm).
l P < 0.001, mouthwash phenol-chloroform versus mouthwash QIAamp kit (N = 25 pairs), McNemar’s exact test for matched pairs.
m Mouthwash phenol-chloroform versus mouthwash Puregene: all pairs had high molecular weight DNA (N = 20 pairs).