Table 3

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 extractionN% samples with high molecular weight DNAaPCR success rate
268 bp536 bp989 bpb
Cytobrushesc
 Phenol-chloroform4055%def100%g97.5h94.4%i
 QIAamp kit402.5%dj100%92.5%89.5%
 NaOH400.0%e40.0%g20.0%h15.0%i
Mouthwashk
 Phenol-chloroform3594.3%flm100%100%100%
 QIAamp kit3013.3%jl100%100%100%
 Puregene kit20100%m100%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).