On 2013 Nov 01, Casey M Bergman commented:

In reviewing the location of P-element insertions in the human genome reported in Table 1 of Majumdar S, 2013, we noticed that the sequences of the P-element target site duplications reported in the paper did not correspond to the sequences observed in the GRCh37/hg19 version of the human genome sequence available at the UCSC Genome Browser.

To resolve this discrepancy, we obtained the original data and methods used to generate the genomic coordinates reported in Table 1 from the authors. Sequence data for integration events catalyzed by the P-element transposase or THAP9 that were mapped from both the 5’ and 3’ end of the P-element insertions are as follows (target site duplication shown in capitals, posted with permission of the authors):

Drosophila P-element Transposase

ctacaaggatgccaagggctgtttcttcagcatggtggGTGGCCATatgtaagcaggtgtgcacacatgtgggcacatgtgctgcat cttgaatgagagctgtgattgttagtgatgtccaggtatgtGTCTGCCAtctcagagtgaccctgagaaaggcattcatttggaagctt tgtttcctgactttgctgtGTGTTCGAtcgtctgttttcaaagtgggatcattagttatgaaggaagatttttcatgaa tttctttccttgtctctgagacgccactttctcctggctctccttctttccgtcggTCTGCCTTttgctctccttttctggttccgtctcacca cgagccactggtggggctcctgccacctccacactgGTCGGCCTcggccacctccacgcctcagggatggggcgcgcgtgccc tctcagtagataatgaggatcactgcagatggcatgatatttagcagactacGGATCTCGagcagtcatccaggatctcaacagtgg

Human THAP9

gtggcgtgatcccagctcactgcaaccTCGGCCTGctcggcttaagtgatcctttcacctcagcttctcaagtagctgggactacag ccctgtccctgtgagtgatgttcccttgttgttccaGTCTCTCTtctctggtcaggaaggtaccactcaatccagggctttctcctggttt gaacttccccagtgagggcctGTGTCTGCattcaggagtgagagtttccccaggagaggagactgaaaagacctgggaaggcaa ccactggactccagcctgggcgacagagcgaTACGTCTCataaaaataaataaataaaacagaaacttaacacaattaaatgactg ataaagaggaatttgtttctccacaccacaaggcctttGTGCGAAGgtgactgtgtgtgtcaacgtcagacagtccctctttctgggag ttaaatgaggttgttagggtggtccatcattcaacatgactgcGGTCGTCCtaacgacaggaaatttgggccccagagacagacac

Using these data, we were able to reproduce the majority of the authors’ results in Table 1 using the default settings of the BLAST service at NCBI for the GRCh37/hg19 version of the human genome in September 2013. However, the same sequence data yielded different coordinates when mapped to either the UCSC Genome Browser (using default BLAT settings) or the Ensembl Genome Browser (using default BLAST settings), with consistent genomic coordinates being reported by both UCSC and Ensembl.

Based on empirical observation and through correspondence with Dr. Deanna Church at NCBI, we learned that results for the organism BLAST service at NCBI prior to mid-September 2013 defaulted to local (scaffold) not global chromosome ("top level") coordinates. Thus, the coordinates of the P-element insertions reported in Table 1 of Majumdar S, 2013 do not accurately reflect the exact location of integration on global chromosomal coordinates.

Based on our re-analysis, the chromosomal location of target site duplications for P-element insertions in the human genome are as follows (GRCh37/hg19, 0-based coordinates):

chrom start end strand

chr17 5024087 5024095 +

chr20 16619371 16619379 +

chr21 17382446 17382454 +

chr11 122102746 122102754 +

chr3 61550440 61550448 +

chr9 25178151 25178159 +

chr14 87818626 87818634 +

chr11 72875900 72875908 +

chr11 79446804 79446812 -

chr15 55619023 55619031 +

chrX 17150535 17150543 +

chr11 11291642 11291650 +

As a consequence of this interchange, NCBI have now updated the default behavior of their organism BLAST service to report global (scaffold) chromosome coordinates, as reported in the 17 Oct 2013 BLASTFeed update.

We thank the authors for making their raw data available and Deanna Church and others at NCBI to help resolve this issue, and thank the authors and Deanna Church for reviewing this comment before posting.

Sincerely,

Casey Bergman

Raquel Linheiro

On 2013 Nov 01, Casey M Bergman commented:

In reviewing the location of P-element insertions in the human genome reported in Table 1 of Majumdar S, 2013, we noticed that the sequences of the P-element target site duplications reported in the paper did not correspond to the sequences observed in the GRCh37/hg19 version of the human genome sequence available at the UCSC Genome Browser.

To resolve this discrepancy, we obtained the original data and methods used to generate the genomic coordinates reported in Table 1 from the authors. Sequence data for integration events catalyzed by the P-element transposase or THAP9 that were mapped from both the 5’ and 3’ end of the P-element insertions are as follows (target site duplication shown in capitals, posted with permission of the authors):

Drosophila P-element Transposase

ctacaaggatgccaagggctgtttcttcagcatggtggGTGGCCATatgtaagcaggtgtgcacacatgtgggcacatgtgctgcat cttgaatgagagctgtgattgttagtgatgtccaggtatgtGTCTGCCAtctcagagtgaccctgagaaaggcattcatttggaagctt tgtttcctgactttgctgtGTGTTCGAtcgtctgttttcaaagtgggatcattagttatgaaggaagatttttcatgaa tttctttccttgtctctgagacgccactttctcctggctctccttctttccgtcggTCTGCCTTttgctctccttttctggttccgtctcacca cgagccactggtggggctcctgccacctccacactgGTCGGCCTcggccacctccacgcctcagggatggggcgcgcgtgccc tctcagtagataatgaggatcactgcagatggcatgatatttagcagactacGGATCTCGagcagtcatccaggatctcaacagtgg

Human THAP9

gtggcgtgatcccagctcactgcaaccTCGGCCTGctcggcttaagtgatcctttcacctcagcttctcaagtagctgggactacag ccctgtccctgtgagtgatgttcccttgttgttccaGTCTCTCTtctctggtcaggaaggtaccactcaatccagggctttctcctggttt gaacttccccagtgagggcctGTGTCTGCattcaggagtgagagtttccccaggagaggagactgaaaagacctgggaaggcaa ccactggactccagcctgggcgacagagcgaTACGTCTCataaaaataaataaataaaacagaaacttaacacaattaaatgactg ataaagaggaatttgtttctccacaccacaaggcctttGTGCGAAGgtgactgtgtgtgtcaacgtcagacagtccctctttctgggag ttaaatgaggttgttagggtggtccatcattcaacatgactgcGGTCGTCCtaacgacaggaaatttgggccccagagacagacac

Using these data, we were able to reproduce the majority of the authors’ results in Table 1 using the default settings of the BLAST service at NCBI for the GRCh37/hg19 version of the human genome in September 2013. However, the same sequence data yielded different coordinates when mapped to either the UCSC Genome Browser (using default BLAT settings) or the Ensembl Genome Browser (using default BLAST settings), with consistent genomic coordinates being reported by both UCSC and Ensembl.

Based on empirical observation and through correspondence with Dr. Deanna Church at NCBI, we learned that results for the organism BLAST service at NCBI prior to mid-September 2013 defaulted to local (scaffold) not global chromosome ("top level") coordinates. Thus, the coordinates of the P-element insertions reported in Table 1 of Majumdar S, 2013 do not accurately reflect the exact location of integration on global chromosomal coordinates.

Based on our re-analysis, the chromosomal location of target site duplications for P-element insertions in the human genome are as follows (GRCh37/hg19, 0-based coordinates):

chrom start end strand

chr17 5024087 5024095 +

chr20 16619371 16619379 +

chr21 17382446 17382454 +

chr11 122102746 122102754 +

chr3 61550440 61550448 +

chr9 25178151 25178159 +

chr14 87818626 87818634 +

chr11 72875900 72875908 +

chr11 79446804 79446812 -

chr15 55619023 55619031 +

chrX 17150535 17150543 +

chr11 11291642 11291650 +

As a consequence of this interchange, NCBI have now updated the default behavior of their organism BLAST service to report global (scaffold) chromosome coordinates, as reported in the 17 Oct 2013 BLASTFeed update.

We thank the authors for making their raw data available and Deanna Church and others at NCBI to help resolve this issue, and thank the authors and Deanna Church for reviewing this comment before posting.

Sincerely,

Casey Bergman

Raquel Linheiro