Dataset Information

Trio-R: a script for assessing maternity and paternity in trio studies performed on Agilent chromosomal microarrays.

ABSTRACT:

Background

Trio studies, which involve the testing of samples from a proband and both parents, are often used by clinical laboratories to help with the classification of genetic variants, including copy number variants. In order for the results of the trio study to be valid, the mother and father must be the true biological parents of the proband. As such, non-paternity and sample mix-ups are potential sources of error. To address these potential issues, we developed a computer script to accurately assess maternity and paternity using single nucleotide polymorphism (SNP) data generated by Agilent chromosomal microarrays, a platform-of-choice for clinical copy number testing.

Results

We assessed the performance of the script on 10 putative trios tested at our laboratory, and found that the numbers and proportions of discordant SNPs were useful for determining parental relationships. The results of the assessment also confirmed maternity and paternity in the 10 trios tested, and by doing so essentially excluded pre-analytical sample switching in these 30 samples.

Conclusions

Computational analysis of SNP data can be implemented as a quality control measure for trio testing performed on Agilent microarrays.

SUBMITTER: Xia D

PROVIDER: S-EPMC6220459 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Publications

Trio-R: a script for assessing maternity and paternity in trio studies performed on Agilent chromosomal microarrays.

Xia Daniel D Zhang Chen C Lip Va V Harris Marian M Shen Yiping Y

BMC medical informatics and decision making 20181106 1

<h4>Background</h4>Trio studies, which involve the testing of samples from a proband and both parents, are often used by clinical laboratories to help with the classification of genetic variants, including copy number variants. In order for the results of the trio study to be valid, the mother and father must be the true biological parents of the proband. As such, non-paternity and sample mix-ups are potential sources of error. To address these potential issues, we developed a computer script to ...[more]

PMID: 30400925

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Project description:We examined copulatory behaviour in the Bonelli´s Eagle (Aquila fasciata) at nesting sites in the eastern zone of the Baetic Cordillera, southern Spain, between 2010 and 2012. We observed the copulatory behaviour of 15 pairs during the pre-laying period. Bonelli´s Eagles commenced sexual activity ca. 69 days before egg-laying. Ninety-six percent of mounting attempts were successful. Bonelli´s Eagle pairs averaged 99.8 copulation attempts per clutch, with an average copulation frequency of 0.86 copulation attempts per day. Pairs displayed a daily bimodal pattern of copulation activity, with copulations occurring most frequently in the evening. We used our data to test three predictions with regard to the paternity assurance hypothesis. Prediction 1, that within-pair copulations increase with local breeding density, was rejected because our models showed no evidence for it. Prediction 2, that within-pair copulations increase during the female fertile period, was marginally supported. Finally, Prediction 3, that mate attendance increases during the female fertile period, was also rejected because mate-guarding did not increase as the fertile period approached. However, mate-guarding was positively correlated with within-pair copulation frequency. Moderate copulation rates compared to other raptors and the absence of mate-guarding suggest that, in the study area, Bonelli´s Eagles exhibit only partially adaptive behaviour to assure their paternity. A possible explanation could be related to the low number of extra-pair encounters observed (opportunities for which appear to be rare), although the gradual increase in within-pair copulations during the female fertile period is consistent with the sperm competition hypothesis. The results are discussed based on the signalling hypothesis, which proposes that raptors signal territory ownership to conspecifics, and possibly to other raptor species, by copulating frequently and conspicuously in the defended nesting area.

Dataset Information

Trio-R: a script for assessing maternity and paternity in trio studies performed on Agilent chromosomal microarrays.

Background

Results

Conclusions

Publications

Trio-R: a script for assessing maternity and paternity in trio studies performed on Agilent chromosomal microarrays.

Similar Datasets

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