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Detection of a genotyping mistake (Hossein Jorjani, 12 June 2014)

We have been informed by one of the sources providing data that a genotyping mistake (at the SNP clustering level) has been discovered that potentially has affected the genotypes of 2254 animals (32%) used in our study (Guo et al., BMC Genetics 2012, 13:82 doi:10.1186/1471-2156-13-... read full comment

Comment on: Guo et al. BMC Genetics, 13:82

Author's erratum (Haroldo Henrique de Rezende Neves, 14 March 2013)

After publication, we figured out that a sentence of the Methods section should be corrected. On Page 3 (2nd paragraph), " half-sib families were split" should be changed to "full-sib families were split" .
We apologize for any confusion. read full comment

Comment on: Neves et al. BMC Genetics, 13:100

Comment on Xu et al (2010) by Tony Waters, Department of Sociology, California State University, Chico Mary Long and Eugene Long, Rong Kwang, Thailand (Tony Waters, 21 February 2013)

Type your comment... read full comment

Comment on: Xu et al. BMC Genetics, 11:18

Some errors (Fuhao Lu, 28 June 2012)

Methods\Genetic diversity and association analysis\End of 2nd Paragraph
Blas2GO -----> Blast2Go
Genious ------> Geneious read full comment

Comment on: Galeano et al. BMC Genetics, 13:48

Editor's comment - further coverage of this research (Simon Harold PhD, 15 May 2012)

Readers may like to be aware of coverage of this research in the scientific press. Please see details on our blog "Digging up the past with ancient DNA":

http://blogs.openaccesscentral.com/blogs/bmcseriesblog/entry/digging_up_the_past_with

Further examples of media coverage can be found here:

http://www.msnbc.msn.com/id/47145013/ns/technology_and_science-science/#.T7JatlKKzcs

http://www.sciencedaily.com/releases/2012/04/120422231826.htm

Simon Harold
Executive Editor
BMC Genetics read full comment

Comment on: Baca et al. BMC Genetics, 13:30

Many thanks (min du, 12 September 2011)

We are appreciated to editors of BioMed Central for their hard work. We believe that the content of this article will be helpful to the development of the MHC research involved in fish. read full comment

Comment on: Du et al. BMC Genetics, 12:78

Correction to Table 3 (Johannes Buitkamp, 28 February 2011)

The frameshift mutation ist located in exon 11, instead of exon 7 as erroneously given in table 3. read full comment

Comment on: Buitkamp et al. BMC Genetics, 12:11

Kronholm et al have published a clarification of this paper (Lou Jost, 14 October 2010)

I would like to alert readers that the authors have published a clarification of this article. See "Correction: Influence of mutation rate on estimators of genetic differentiation-lessons from Aradidopsis thaliana",
http://www.biomedcentral.com/content/pdf/1471-2156-11-88.pdf

This clears up some potential misunderstandings about the nature of differentiation and its estimators. read full comment

Comment on: Kronholm et al. BMC Genetics, 11:33

A little comfusion (Tsin Ho, 11 January 2010)

"Two lines independently transformed by this cosmid (5581.118 and 5581.4), each with a single independent autosomal insertion, were obtained and tested for complementation of swit476. Neither of them was able to complement swit476, implying that a6, b6, CG14798 and EG:9D2.4 are not swi."
I don't comprehend these words. If the two fragments didn't complement the swit476, the loci on these fragments and the swi should be functional alleles. read full comment

Comment on: Schwartz et al. BMC Genetics, 5:15

Fails to adress the likely Anatolian origin (Luis Aldamiz, 16 December 2009)

I must say that I'm again disappointed at the approach of the paper. Arabs and Europeans are used as controls but a large void is left (again) in the area around modern Turkey, where the ancient Jewish Diaspora lived for many centuries (in a time when proselytism was common in Judaism too).

I find this most striking but also systematic failure of Jewish genetic studies in general. Only studies no focused in Jewish ancestry, like Bauchet 2007, have provided some clarification on this aspect, clustering Jews with Greeks and Armenians. But they await to be confirmed.

The first thing I looked for in this paper was whether Turks (or maybe Balcanic peoples) had been sampled as controls. Sadly it was not the case.

Otherwise the paper does provide some... read full comment

Comment on: Kopelman et al. BMC Genetics, 10:80

Figure 4 has the text mixed up between parts A, B, and C (Cameron Gundry, 16 March 2009)

Figure 4 has the text mixed up between parts A, B. 4A is the unlabeled probe data, which has more noise than typically seen. 4B is for scanning.

The figure 4 legend should read as follows:
"Figure 4. Simultaneous genotyping of common SNP rs9894946 and rare SNP rs17883532. A. In genotyping mode using an unlabeled probe for rs9894946, the 3 genotypes are distinguisable (CC in gray, CT in red, TT in blue). B. In mutation scanning mode, heterozygous samples for either the first (in red) or the second SNP (in green) have virtually indistinguishable melting curves. C. Mutation scanning of homozygous rs9894946 CC subset reveals heterozygous rs17883532 CT (In green)." read full comment

Comment on: Garritano et al. BMC Genetics, 10:5

Iranian have no Y-SNP HG D (Hai LAN, 01 August 2008)

Dear editor, After reading this paper ,i found that there is a tiny mistake on the Y-SNP Data. According to Wells's paper (2001),Iranian have 19% of HG E ,not HG D. I'm a Chinese and really care about HG D,so..... your LAN Hai read full comment

Comment on: Marchani et al. BMC Genetics, 9:47

Lewontin and Kojima 1960 (Graham Poulter, 17 June 2008)

Another reference which looks relevant to the problem, using adaptive topography and differential equations:The Evolutionary Dynamics of Complex PolymorphismsR. C. Lewontin and Ken-ichi KojimaEvolution, Vol. 14, No. 4 (Dec., 1960), pp. 458-472http://www.jstor.org/stable/2405995?seq=1 read full comment

Comment on: Hallgrímsdóttir et al. BMC Genetics, 9:17

Authors' erratum (Jessica Woo, 28 January 2008)

Readers, After publication we discovered an erratum in the discussion. On page 3, first column, a sentence should be changed to: "While we did not specifically quantitate non-human DNA in our samples, the high call rates we and others have reported for buccal samples suggest that bacterial contamination may, in fact, be a minor issue, perhaps due to the human-specific probes employed in large-scale genotyping." This change will be included in the XML and PDF versions of the published article within the next few weeks to months.We apologize for any confusion.Jessica Woo read full comment

Comment on: Woo et al. BMC Genetics, 8:79

Correction: typographical error (Ryan Garrick, 05 December 2006)

Results: Tests of recombination and selective neutrality (Page 5 of 15) Text: “At SmEF-1α, significant evidence for recombination (P < 0.01, Table 6) was detected for three pairwise comparisons involving four of the 21 alleles resolved (A11–A13, A11– A14 and A3–A13). Because three of these alleles occur only in the BR population (i.e. A13, A16 and A18, Table 4)*, which is likely to have been isolated for a long time [31], phylogeographic signal may be relatively unaffected [25]”.* Typographical error: "(i.e. A13, A16 and A18, Table 4)" Correction: "(i.e. A11, A13 and A14, Table 4)" * This typographical error is restricted to the above paragraph only, and results are not affected in any way. The primary author takes full responsibility for this error. read full comment

Comment on: Garrick et al. BMC Genetics, 7:11

Origin of Indian caste system! (T Srinath, 01 September 2006)

The article has a shallow depth of analysis, only based on AMOVA (analysis of molecular variance) authors’ tried to make a bulletproof conclusion on structuring of Indian populations. 1. The extensive study of India by Metspalu et al. 2004 observed a very low frequency of Western Eurasian haplogroups in India both castes as well as in tribes while, authors’ found a comparatively higher frequency in Upper castes without any literature survey. 2. The 85% presence of Y chromosomal haplogroup H in hierarchal Hindu Caste system is a serious observation which needs to be clarified. 3. In figure legend 1. 16517 should be 16519. In supplementary 2. The W36 haplotype should be from K haplogroup and this should also change in Fig.1. The presence of 15670 (M2 marker) in several... read full comment

Comment on: Thanseem et al. BMC Genetics, 7:42

O2a-M95 Clade (Balaji Athreyan, 25 August 2006)

(1) There are a couple of minor typographical errors. The authors refer to the "J172 clad" instead of "J172 clade". In another place they write "sister clads" instead of "sister clades".(2) The authors assume that the O2a-M95 clade dates to the initial settlement of the Indian subcontinent by moderen humans some 60,000 years ago and that this clade spread to Southeast Asia from India. This is highly unlikely.The two excellent papers on Indian Y-chromosomes earlier this year, Sahoo et al., Proc. Nat. Acad. Sci., vol. 103, no. 4, 843-848, Jan. 2006 and Sengupta et al., Am. J. Hum. Gen., vol. 78, 202-221, Feb. 2006 both suggest an exogenous origin for M95.It is most likely that migrants from Southeast Asia speaking Austro-Asiatic langauges introduced this clade to India via the Northeast... read full comment

Comment on: Thanseem et al. BMC Genetics, 7:42

Update on linkage map given genome sequence assembly (Mohamed Noor, 07 February 2006)

Since the publication of our linkage map [1], the genome of Drosophila mojavensis has been sequenced and assembled (see http://rana.lbl.gov/drosophila/tools.html). The physical assembly matches very well with our linkage map overall. We have prepared this comment to note a handful of minor inconsistencies between our linkage map and the new physical assembly.First, sequences of four of the unmapped microsatellites that we suggested to be probably autosomal were assembled into contigs associated with the X-chromosome. These markers are DMOJA500, DMOJA513, DMOJA514, and DMOJA517. None of the microsatellites we localized to the X were assembled onto autosomal scaffolds, and none of the microsatellites we assigned to a particular chromosome based on our linkage map were assembled onto a... read full comment

Comment on: Staten et al. BMC Genetics, 5:12

Update (Matthias Wjst, 30 May 2005)

The annotation pipeline is now available for any region in the human genome, please click. read full comment

Comment on: Wjst BMC Genetics, 6:2

Mitochondrial footsteps of the Old World human colonization: A single origin, several dispersal hypothesis. José M. Larruga, Ana M. González, Nicole Maca-Meyer, Carlos Flores and Vicente M. Cabrera (Vicente Cabrera, 29 October 2004)

The hypothesis that Homo s. sapiens originated in Africa and later colonized Eurasia replacing the descendents of H. erectus is now widely accepted. However, the timing of the exit out of Africa and the routes taken remain controversial. Archaeological and genetic evidence (Cavalli-Sforza et al. 1994) support two dispersals from Africa. A southern migration that coasting Asia reached Australia, and a northern migration that reached Western Asia through the Near East. Studies based on complete mitochondrial DNA sequences indubitably demonstrated that only two macrolineages, M and N, comprise all the mitochondrial variation existing out of Africa (Ingman et al. 2000; Maca-Meyer et al. 2001; Herrnstadt et al. 2002). Based on the phylogeographic distribution of these two... read full comment

Comment on: Maca-Meyer et al. BMC Genetics, 2:13

Discrepancy in PCR methodology (Manjusha Dixit, 03 February 2004)

We read paper by Chhabra et al. (1) and found it very interesting but we would like to draw the attention of authors towards some points. Firstly, primer sequences used for amplification of desired region of Apolipoprotein CIII gene does not match with the sequences given in reference article (2). Sequences reported in the paper are, forward primer: 5'- CAT GGT TGC CTA CAG GAG TTC-3' and reverse: 3'-TGA CCT TCC GCA CAA AGC TGT-5', but in reference article reverse primer is 5'-TGA CCT TCC GCA CAA AGC TGT-3'. Secondly, sequence of forward primer does not show 100% match with any of the Apo CIII gene entries in NCBI database. For example with a sequence " accession XO1392.1 GI:28725", only bases 1-15 of forward primer match with base 2955-2969 and bases 16-21 match with base 2972-2977. In... read full comment

Comment on: Chhabra et al. BMC Genetics, 3:9