State of the Art for Microhaplotypes
Round 1
Reviewer 1 Report
Genes-1813393 - State of the Art for Microhaplotypes
The authors review the current state of Microhaplotypes for use in the forensic DNA community.
The review focuses on four aspects: Individualization, Ancestry Inference, Kinship Analysis, and Mixture Deconvolution.
The review is well written and I only have one suggestion for the authors to consider. In the future directions section, the deconvolution of higher order mixtures, even with microhaplotypes, will likely require probabilistic methods of interpretation to remove biases of comparing a Person of Interest to the evidence. Perhaps the authors could speculate on the potential of using software solutions in the future.
Congratulations for an excellent review of this topic.
Author Response
Response to Reviewer 1
We thank the reviewer for the positive comment and for raising the issue of statistics in complex mixtures. We have added a paragraph in the Future Directions section commenting on the necessity of developing probabilistic genotyping for mixture analysis.
Reviewer 2 Report
The manuscript is of high quality, short, and clear. I only have a few suggestions.
The titles of the figures should be placed below the figures (the titles are placed above figures 1, 3, 4, 5, and 6).
The formats of the numbers in the titles should be the same (Fig. 4: ’.. 6 ..’, Fig. 5: ’.. six ..’) .
Author Response
Response to Reviewer 2
(1) We have moved the caption/titles to a consistent position below all of the Figures and the Table.
(2) We have also made the formats referencing the figures more uniform. The Tracking Change feature of the editor was turned on to make it easy to identify the revisions.
Reviewer 3 Report
This paper reviews the state of the art for microhaplotypes studies in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. With integrated data and synthetic analysis, the authors draw the conclusion that a panel of higher Ae microhaplotypes can outperform the standard CODIS 20 markers.
It is understandable that the study focuses on the efficiency of MHs in forensic application, but as a review it might be more comprehensive.
Minor opinions：
1. The sequencing platforms and technologies used in MHs should be compared and discussed, because the effective read length (influenced by the decreased sequencing quality of the read end, the overlap mapping quality of PE reads, and so on) are crucial to the accuracy and efficiency of MHs. In other words, the effective read length itself determines the length of genetic region that can be used to construct MH, i.e., the reliable region providing diversity or so-called Ae, and then the genomic screening strategy.
2. In addition to increasing marker numbers or Ae for complex kinship analysis and mixture deconvolution, another feasible way is to combine multiple types of markers to complement each other. As a specific and effective marker, MH has its advantages and limitations, how to use it with the current marker system needs further discussion.
Author Response
Response to Reviewer 3
[Minor opinion 1] We agree that a full review of MHs in general would consider the methodology for typing MHs, but that is not the objective of this paper. As stated in the last line of the Introduction, we are considering “briefly the state of the art in each of four main areas of forensic” applications. We think a methodology review considering the molecular, laboratory, and biostatistical aspects of MH typing is needed, but we are not prepared to write such a review.
[Minor opinion 2] We certainly agree with the reviewer. See our inserts on pages 8 and 12. We recently published a paper advocating joint typing by MPS of the CODIS markers and a panel of 24 MH [reference 13 in the manuscript]. We have added to this manuscript sentences that note large SNP chips will remain more powerful than MHs for distant relationships and noting that SNPs as well as STRs can be analyzed with MH.
