scholarly journals Impact of SNP microarray analysis of compromised DNA on kinship classification success in the context of investigative genetic genealogy

2021 ◽  
Author(s):  
Jard Hemmo de Vries ◽  
Daniel Kling ◽  
Athina Vidaki ◽  
Pascal Arp ◽  
Vivian Kalamara ◽  
...  
Keyword(s):  
Microarray Analysis ◽  
Fragment Size ◽  
False Negative ◽  
Dna Amount ◽  
Genomic Databases ◽  
Genetic Genealogy ◽  
Snp Microarray ◽  
Dna Quality ◽  
Snp Data ◽  
The Impact

Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relatively high input DNA quantity and quality, while SNP microarray data from compromised DNA typically obtainable from crime scene stains are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of SNP microarray analysis of deprecated DNA on kinship classification success, as relevant in IGG. Reference data from manufacturer-recommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 nanogram to 6.25 picogram led to decreased SNP call rates and increased genotyping errors, kinship classification success did not decrease down to 250 picogram for siblings and 1st cousins, 1 nanogram for 2nd cousins, while at 25 picogram and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800-200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false positive ones.

scholarly journals Impact of SNP microarray analysis of compromised DNA on kinship classification success in the context of investigative genetic genealogy

2021 ◽  
pp. 102625
Author(s):  
Jard H. de Vries ◽  
Daniel Kling ◽  
Athina Vidaki ◽  
Pascal Arp ◽  
Vivian Kalamara ◽  
...  
Keyword(s):  
Microarray Analysis ◽  
Genetic Genealogy ◽  
Snp Microarray

scholarly journals Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 146
Author(s):  
Catarina Xavier ◽  
Mayra Eduardoff ◽  
Barbara Bertoglio ◽  
Christina Amory ◽  
Cordula Berger ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Method ◽  
Fragment Size ◽  
Molecular Genetic ◽  
Extraction Methods ◽  
Degraded Dna ◽  
Size Analysis ◽  
Dna Fragments ◽  
Dna Amount

The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.

scholarly journals T stage-dependent lymph node and distant metastasis and the accuracy of lymph node assessment in rectal cancer

2021 ◽  
Author(s):  
Henry Ptok ◽  
Frank Meyer ◽  
Roland S. Croner ◽  
Ingo Gastinger ◽  
Benjamin Garlipp
Keyword(s):  
Rectal Cancer ◽  
Overall Survival ◽  
Lymph Node ◽  
Lymph Nodes ◽  
False Negative ◽  
Cumulative Risk ◽  
Distant Metastases ◽  
Number Of Patients ◽  
Tumor Stages ◽  
The Impact

Summary Objective To analyze data obtained in a representative number of patients with primary rectal cancer with respect to lymph node diagnostics and related tumor stages. Methods In pT2-, pT3-, and pT4 rectal cancer lesions, the impact of investigated lymph nodes on the frequency of pN+ status, the cumulative risk of metachronous distant metastases, and overall survival was studied by means of a prospective multicenter observational study over a defined period of time. Results From 2000 to 2011, the proportion of surgical specimens with ≥ 12 investigated lymph nodes increased significantly, from 73.6% to 93.2% (p < 0.001; the number of investigated lymph nodes from 16.2 to 20.8; p < 0.001). Despite this, the percentage of pN+ rectal cancer lesions varied only non-significantly (39.9% to 45.9%; p = 0.130; median, 44.1%). For pT2-, pT3-, and pT4 rectal cancer lesions, there was an increasing proportion of pN+ findings correlating significantly with the number of investigated lymph nodes up to n = 12 investigated lymph nodes. Only in pT3 rectal cancer was there a significant increase in pN+ findings in case of > 12 lymph nodes (p = 0.001), but not in pT2 (p = 0.655) and pT4 cancer lesions (p = 0.256). For pT3pN0cM0 rectal cancer, the risk of metachronous distant metastases and overall survival did not depend on the number of investigated lymph nodes. Conclusion In rectal cancer, at least n = 12 lymph nodes are to be minimally investigated. The investigation of fewer lymph nodes is associated with a higher risk of false-negative pN0 findings. In particular, in pT3 rectal cancer, the investigation of more than 12 lymph nodes lowers the risk of false-negative pN0 findings. An upstaging effect by the investigation of a possibly maximal number of lymph nodes could not be detected.

scholarly journals Performance of Unobserved Self-Collected Nasal Swabs for Detection of SARS-CoV-2 by RT-PCR Utilizing a Remote Specimen Collection Strategy

2021 ◽  
Author(s):  
Ron M Kagan ◽  
Amy A Rogers ◽  
Gwynngelle A Borillo ◽  
Nigel J Clarke ◽  
Elizabeth M Marlowe
Keyword(s):  
Return To Work ◽  
Screening Program ◽  
False Negative ◽  
N Gene ◽  
Rt Pcr ◽  
Pooled Testing ◽  
Specimen Collection ◽  
Asymptomatic Patients ◽  
Nasal Swabs ◽  
The Impact

Abstract Background The use of a remote specimen collection strategy employing a kit designed for unobserved self-collection for SARS-CoV-2 RT-PCR can decrease the use of PPE and exposure risk. To assess the impact of unobserved specimen self-collection on test performance, we examined results from a SARS-CoV-2 qualitative RT-PCR test for self-collected specimens from participants in a return-to-work screening program and assessed the impact of a pooled testing strategy in this cohort. Methods Self-collected anterior nasal swabs from employee return to work programs were tested using the Quest Diagnostics SARS-CoV-2 RT-PCR EUA. The Ct values for the N1 and N3 N-gene targets and a human RNase P (RP) gene control target were tabulated. For comparison, we utilized Ct values from a cohort of HCP-collected specimens from patients with and without COVID-19 symptoms. Results Among 47,923 participants, 1.8% were positive. RP failed to amplify for 13/115,435 (0.011%) specimens. The median (IQR) Cts were 32.7 (25.0-35.7) for N1 and 31.3 (23.8-34.2) for N3. Median Ct values in the self-collected cohort were significantly higher than those of symptomatic, but not asymptomatic patients. Based on Ct values, pooled testing with 4 specimens would have yielded inconclusive results in 67/1,268 (5.2%) specimens but only a single false-negative result. Conclusions Unobserved self-collection of nasal swabs provides adequate sampling for SARS-CoV-2 RT-PCR testing. These findings alleviate concerns of increased false negatives in this context. Specimen pooling could be used for this population as the likelihood of false negative results is very low due when using a sensitive, dual-target methodology.

scholarly journals Impact of repeated nasal sampling on detection and quantification of SARS-CoV-2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Joshua M. Levy ◽  
Jennifer K. Frediani ◽  
Erika A. Tyburski ◽  
Anna Wood ◽  
Janet Figueroa ◽  
...  
Keyword(s):  
Test Performance ◽  
Perceived Risk ◽  
False Negative ◽  
Sample Collection ◽  
Diagnostic Assays ◽  
Negative Findings ◽  
High Concordance ◽  
Repeated Sample ◽  
Multiple Samples ◽  
The Impact

AbstractThe impact of repeated sample collection on COVID-19 test performance is unknown. The FDA and CDC currently recommend the primary collection of diagnostic samples to minimize the perceived risk of false-negative findings. We therefore evaluated the association between repeated sample collection and test performance among 325 symptomatic patients undergoing COVID-19 testing in Atlanta, GA. High concordance was found between consecutively collected mid-turbinate samples with both molecular (n = 74, 100% concordance) and antigen-based (n = 147, 97% concordance, kappa = 0.95, CI = 0.88–1.00) diagnostic assays. Repeated sample collection does not decrease COVID-19 test performance, demonstrating that multiple samples can be collected for assay validation and clinical diagnosis.

scholarly journals Integrated Genomic Analysis of Sézary Syndrome

2011 ◽  
Vol 2011 ◽  
pp. 1-13 ◽  
Author(s):  
Xin Mao ◽  
Tracy Chaplin ◽  
Bryan D. Young
Keyword(s):  
Copy Number ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Sézary Syndrome ◽  
Sezary Syndrome ◽  
Snp Microarray ◽  
The Impact ◽  
Chromosome Regions

Sézary syndrome (SS) is a rare variant of primary cutaneous T-cell lymphoma. Little is known about the underlying pathogenesis of S. To address this issue, we used Affymetrix 10K SNP microarray to analyse 13 DNA samples isolated from 8 SS patients and qPCR with ABI TaqMan SNP genotyping assays for the validation of the SNP microarray results. In addition, we tested the impact of SNP loss of heterozygosity (LOH) identified in SS cases on the gene expression profiles of SS cases detected with Affymetrix GeneChip U133A. The results showed: (1) frequent SNP copy number change and LOH involving 1, 2p, 3, 4q, 5q, 6, 7p, 8, 9, 10, 11, 12q, 13, 14, 16q, 17, and 20, (2) reduced SNP copy number at FAT gene (4q35) in 75% of SS cases, and (3) the separation of all SS cases from normal control samples by SNP LOH gene clusters at chromosome regions of 9q31q34, 10p11q26, and 13q11q12. These findings provide some intriguing information for our current understanding of the molecular pathogenesis of this tumour and suggest the possibility of presence of functional SNP LOH in SS tumour cells.

scholarly journals The 28 + 28 day design is an effective sampling time for analyzing mutant frequencies in rapidly proliferating tissues of MutaMouse animals

2021 ◽  
Vol 95 (3) ◽  
pp. 1103-1116
Author(s):  
Francesco Marchetti ◽  
Gu Zhou ◽  
Danielle LeBlanc ◽  
Paul A. White ◽  
Andrew Williams ◽  
...  
Keyword(s):  
Germ Cells ◽  
False Negative ◽  
Sampling Time ◽  
Male Germ Cells ◽  
Negative Results ◽  
False Negative Results ◽  
Detection Of Mutations ◽  
The Impact ◽  
Sampling Times

AbstractThe Organisation for Economic Co-Operation and Development Test Guideline 488 (TG 488) uses transgenic rodent models to generate in vivo mutagenesis data for regulatory submission. The recommended design in TG 488, 28 consecutive daily exposures with tissue sampling three days later (28 + 3d), is optimized for rapidly proliferating tissues such as bone marrow (BM). A sampling time of 28 days (28 + 28d) is considered more appropriate for slowly proliferating tissues (e.g., liver) and male germ cells. We evaluated the impact of the sampling time on mutant frequencies (MF) in the BM of MutaMouse males exposed for 28 days to benzo[a]pyrene (BaP), procarbazine (PRC), isopropyl methanesulfonate (iPMS), or triethylenemelamine (TEM) in dose–response studies. BM samples were collected + 3d, + 28d, + 42d or + 70d post exposure and MF quantified using the lacZ assay. All chemicals significantly increased MF with maximum fold increases at 28 + 3d of 162.9, 6.6, 4.7 and 2.8 for BaP, PRC, iPMS and TEM, respectively. MF were relatively stable over the time period investigated, although they were significantly increased only at 28 + 3d and 28 + 28d for TEM. Benchmark dose (BMD) modelling generated overlapping BMD confidence intervals among the four sampling times for each chemical. These results demonstrate that the sampling time does not affect the detection of mutations for strong mutagens. However, for mutagens that produce small increases in MF, sampling times greater than 28 days may produce false-negative results. Thus, the 28 + 28d protocol represents a unifying protocol for simultaneously assessing mutations in rapidly and slowly proliferating somatic tissues and male germ cells.

Concurrent Loss of Heterozygosity and Mosaic Deletion of 12p13.32pter

2016 ◽  
Vol 148 (2-3) ◽  
pp. 174-178
Author(s):  
Rosana S. Faria ◽  
Claudiner P. de Oliveira ◽  
Marcella M. da Costa ◽  
Maria T.A. da S. Rosa ◽  
Mara S. Córdoba ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Microarray Analysis ◽  
Array Cgh ◽  
Distal Segment ◽  
Chromosome 12 ◽  
Chromosome Microarray Analysis ◽  
Complex Rearrangement ◽  
Snp Data ◽  
Break Induced Replication ◽  
Chromosome Microarray

Deletions in the short arm of chromosome 12 are the rarest subtelomeric imbalances. Less than 20 patients have been reported to date, and their microdeletions were identified either by FISH or array-CGH without SNP data. Here, we report a patient with a 12p13.32pter mosaic deletion detected by chromosome microarray analysis with loss of heterozygosity (LOH) of the deleted segment in addition to the adjacent distal segment. LOH is indicative of a complex rearrangement, suggestive of mitotic microhomology-mediated break-induced replication.

Nipple Confusion

PEDIATRICS ◽  
1993 ◽  
Vol 92 (2) ◽  
pp. 300-301
Author(s):  
DOREN FREDRICKSON
Keyword(s):  
Breast Feeding ◽  
Statistical Power ◽  
White Women ◽  
Small Sample Size ◽  
False Negative ◽  
Small Sample ◽  
Bottle Feeding ◽  
Feeding Duration ◽  
Breast Feed ◽  
The Impact

To the Editor.— I wish to comment on the study reported by Cronenwett et al,1 which was a fascinating prospective study among married white women who planned to breast-feed. Women were randomly selected to perform either exdusive breast-feeding or partial breast-feeding with bottled human milk supplements to determine the impact of infant temperament and limited bottle-feeding on breast-feeding duration. The authors admit that small sample size and lack of statistical power make a false-negative possible.

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