Distributions of the minimum KI, the maximum KI, and the true KI for (a) Parent-Child and (b) Full-Sib relationships with 13 CODIS core loci.

<p>The related pairs were simulated with Caucasian data, and KIs were calculated with African American, Caucasian, southeastern Hispanic, and southwestern Hispanic population data.</p

False positive rates of the SWGDAM recommendation 6 strategy and the minimum KI≥KI threshold strategy (i.e., KIs of 1,000 and 10,000) based on 13 CODIS core loci and Caucasian population data for different sizes of databases from 10,000 to 1 million profiles.

<p>False positive rates of the SWGDAM recommendation 6 strategy and the minimum KI≥KI threshold strategy (i.e., KIs of 1,000 and 10,000) based on 13 CODIS core loci and Caucasian population data for different sizes of databases from 10,000 to 1 million profiles.</p

False negative rates of using jointly IBS≥16 and KI based methods, including the SWGDAM recommendation 6 strategy and the minimum KI≥KI threshold strategy (i.e., Kis of 1,000, 10,000 and 100,000), based on 13 CODIS core loci and Caucasian population data for different sizes of databases from 100,000 to 10 million profiles.

<p>The false negative rate is from 0.4 to 1 in the Y axis.</p

False negative rates of the SWGDAM recommendation 6 strategy and the minimum KI≥KI threshold strategy (i.e., KIs of 1,000, 10,000, and 100,000) based on 13 CODIS core loci and Caucasian population data for different sizes of databases from 10,000 to 1 million profiles.

<p>X axis is the log₁₀(N); N is the database size. Y axis is the false negative rates (i.e., proportions of true relationships excluded) of the strategies.</p

Counts of the minimum and maximum KIs of the mother-child pairs using empirical data.

<p>N is the total number of pairs per population. For example, in all 112 African American mother-child pairs, there are 11 pairs had the minimum KI associated with Caucasian population data.</p><p>a) Note that there was no empirical mother child pairs for southeastern Hispanics.</p

False positive rates of the SWGDAM recommendation 6 stragety and the minimum KI≥KI threshold strategy (i.e., KIs of 10,000 and 100,000) based on 15 STR loci (i.e., 13 CODIS core loci, D2S1338, and D19S433) and Caucasian population data for different sizes of databases from 100,000 to 10 million profiles.

<p>False positive rates of the SWGDAM recommendation 6 stragety and the minimum KI≥KI threshold strategy (i.e., KIs of 10,000 and 100,000) based on 15 STR loci (i.e., 13 CODIS core loci, D2S1338, and D19S433) and Caucasian population data for different sizes of databases from 100,000 to 10 million profiles.</p

False negative rates of the SWGDAM recommendation 6 strategy and the minimum KI≥KI threshold strategy (i.e., KIs of 1,000, 10,000, and 100,000) based on 13 CODIS core loci and Caucasian population data for different sizes of databases from 100,000 to 10 million profiles.

<p>False negative rates of the SWGDAM recommendation 6 strategy and the minimum KI≥KI threshold strategy (i.e., KIs of 1,000, 10,000, and 100,000) based on 13 CODIS core loci and Caucasian population data for different sizes of databases from 100,000 to 10 million profiles.</p

Accuracies of the minimum and maximum KIs being the true KI per population by simulations.

<p>For example, for true unrelated pairs identified as parent-child, if the true population is African American and four KIs are calculated with each of the four major populations, there is an 82.1% chance that the minimum KI is obtained with the true population (i.e., African American) and a 17.9% (i.e., 1–82.1%) chance that the minimum KI is obtained with any of the other populations. Likewise, for true parent-child pairs, if the true population is African American and four KIs are calculated with each of the four major populations, there is a 74.9% chance that the minimum KI is obtained with the true population (i.e., African American) and a 25.1% (i.e., 1–74.9%) chance that the minimum KI is obtained with any of the other populations.</p

Table3_TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.XLSX

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.</p

Table2_TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.XLSX

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.</p