Comparison of biological specimens and DNA collection methods for PCR amplification and microarray analysis

Rethmeyer, Jasmine; Tan, Xiaoyu; Manzardo, Ann M.; Schroeder, Stephen R.; Butler, Merlin G.

doi:10.1515/cclm-2012-0429

Cited by 8 publications

(6 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Buccal cheek swabs for DNA microarray analysis were also taken on each child, in order to find possible genetic syndromes that might not have been observed clinically. DNA has been isolated on a subset of children for DNA structural microarray analysis following established protocol (Rethmeyer, Tan, Manzardo, Schroeder, & Butler, 2012). Results have been submitted for separate publication (Usrey, Manzardo, Roberts, Schroeder, & Butler, under review).…”

Section: Methodsmentioning

confidence: 99%

Risk Factors for Self-Injury, Aggression, and Stereotyped Behavior Among Young Children At Risk for Intellectual and Developmental Disabilities

Schroeder¹,

Marquis²,

Reese³

et al. 2014

American Journal on Intellectual and Developmental Disabilities

Self Cite

View full text Add to dashboard Cite

Before the 1990s, research on the early identification and prevention of severe behavior disorders (SBDs), such as aggression, self-injury, and stereotyped behavior, among young children with intellectual and developmental disabilities (IDD), was mostly done with children 3 years or older. More recent work suggests that signs of SBDs may occur as early as 6 months in some infants. The present study combined a cross-sectional and longitudinal approach to examine SBDs in 180 young children aged 4–48 months recruited through mass screening, then receiving an interdisciplinary evaluation and six-month follow-ups for one year. Twelve potential risk factors related to SBDs were examined. Eight of these risk factors, including age, gender, diagnosis, intellectual and communication levels, visual impairment, parent education, family income, were differentially related to scores for Aggression, SIB, and Stereotyped Behavior subscales on the Behavior Problems Inventory (BPI-01) at initial interdisciplinary evaluation. BPI-01 scores decreased over the year for 57% of the children and increased for 43%. The amount of decrease on each BPI-01 subscale varied with age, gender, and diagnosis.

show abstract

Section: Methodsmentioning

confidence: 99%

Risk Factors for Self-Injury, Aggression, and Stereotyped Behavior Among Young Children At Risk for Intellectual and Developmental Disabilities

Schroeder¹,

Marquis²,

Reese³

et al. 2014

American Journal on Intellectual and Developmental Disabilities

Self Cite

View full text Add to dashboard Cite

show abstract

“…Whole exome sequencing from buccal swab-extracted DNA was successfully carried out using Ion Torrent18 and Illumina19 systems. Good performances were also reported for HLA-genotyping,20 chromosomal microarray,21 and genome-wide chip array 22. Overall, the collection of buccal mucosa epithelial cells performed via swabbing emerged as a cost-effective method due to the ease of the collection procedure and to the better stability for shipping and storage.…”

Section: Resultsmentioning

confidence: 99%

BRCAtesting on buccal swab to improve access to healthcare and cancer prevention: a performance evaluation

Paolis

Perrucci

Marchetti

et al. 2022

Int J Gynecol Cancer

View full text Add to dashboard Cite

ObjectiveBRCA1/2 (BRCA) genetic testing allows patients with high-grade serous ovarian cancer to receive appropriate medical management with molecular target therapy and prevention strategies. Most of the BRCA sequencing methods use blood as the primary source of germline DNA. Buccal swab emerged as an alternative collection device due to its convenient and non-invasive characteristics. This study assessed the suitability of buccal swabs as the DNA source in next-generation sequencing-based BRCA genotyping.MethodsMatched buccal swabs and blood samples were collected from 51 patients with high-grade serous ovarian cancer, including 29 BRCA-mutated patients, from June to December 2021. Buccal swabs were self-collected using COPAN FLOQSwabs hDNA Free. BRCA genes were amplified using Devyser’s BRCA next-generation sequencing kit and sequenced on the Illumina MiSeq platform. We evaluated collection and extraction procedures, amplification and sequencing performances, coverage data, blood/swab variant calling concordance, and interpretation.ResultsComparable sequencing parameters were observed between the two sample types in term of mean total number of reads passing filter for indexed sample (p>0.05) and sequencing coverage distribution, with a widespread overlap of mean depth of coverage/target region between blood and swab samples. An overall concordance of 100% in both polymorphisms and pathogenic variants calling between the two DNA sources were observed, including the copy number variation prediction.ConclusionsData from this study support the use of buccal swabs as an alternative source of DNA for BRCA evaluation. The use of this alternative delivery mode of BRCA testing may facilitate access to care without compromising patient outcomes.

show abstract

“…In the case of fast typifying of human samples for forensic analysis it should be noted that human samples are more complex than the proposed 74 bases synthetic sequence, usually presenting the genome in a double strand structure with high packing, safeguarded inside the cell's nucleus. Also, while the detection limits achieved are optimal for our synthetic sequence, the total genetic material found per human cell can be very low (between 3 and 6 picograms per cell) and the amount of cells that can be found in human samples can vary significantly, depending on the sample origins 41 , being this scenario a limitation of this technology in its current configuration. Therefore, for the incorporation of real human samples, research on the integration and the optimization of extraction methods (Chelex 42 ) and DNA denaturalization methods (chemical denaturalization 43 ) inside the paper supports would be necessary.…”

Section: Discussionmentioning

confidence: 99%

Naked eye Y amelogenin gene fragment detection using DNAzymes on a paper-based device

Azuaje-Hualde

Arroyo-Jimenez

Garai-Ibabe

et al. 2020

Analytica Chimica Acta

View full text Add to dashboard Cite

Nowadays, there are strong efforts in developing new technology for rapid detection of specific DNA sequences for environmental monitoring, forensic analysis and rapid biomedical diagnosis applications. That is where microfluidic paper-based analytical devices are positioned as suitable platforms for the development of point of care analytical devices, due to their simple fabrication protocols, ease of use and low cost. Herein, a methodology for in situ single strand DNA detection by using a colorimetric assay based on the formation of a DNAzyme within a paper substrate was developed. A DNAzyme that could only be formed in the presence of a specific sequence of the Y human amelogenin gene was designed. The performance of the DNAzyme was followed colorimetrically first in solution and then in paper substrates. The reaction was found to be specific to the Y fragment selected as analyte. The DNAzyme reaction on paper enabled the unequivocal colorimetric identification of the Y single strand DNA fragment both qualitatively, with the naked eye (143 ng), and quantitatively by image analysis (45.7 ng). As a proof of concept, a microfluidic paper-based device, pre-loaded with all DNAzyme reagents, was characterized and implemented for the simultaneous detection of X and Y single strand DNA fragments.

show abstract

Comparison of biological specimens and DNA collection methods for PCR amplification and microarray analysis

Cited by 8 publications

References 8 publications

Risk Factors for Self-Injury, Aggression, and Stereotyped Behavior Among Young Children At Risk for Intellectual and Developmental Disabilities

Risk Factors for Self-Injury, Aggression, and Stereotyped Behavior Among Young Children At Risk for Intellectual and Developmental Disabilities

BRCAtesting on buccal swab to improve access to healthcare and cancer prevention: a performance evaluation

Naked eye Y amelogenin gene fragment detection using DNAzymes on a paper-based device

Contact Info

Product

Resources

About