On 2015 Oct 22, Horacio Rivera commented:

A de novo inv dup(1) turns out to be a rea(1)dup q chromosome I remark that the de novo mosaic 1q32→qter duplication onto 1pter (concomitant with a normal clone) described by Levy et al. [2015] is not an inverted duplication because direct and inverted duplications are officially defined as “a gain of a chromosomal segment observed at the original chromosome location” [Shaffer et al., 2013], not to mention that the orientation of the extra segment was indeed a direct one. It is significant that in their discussion, Lévy et al. [2015] refer to three other similar chromosome-1 rearrangements entailing an 1q duplication (although none with interstitial telomeric repeats) and visualize them as “recombinants” from an hypothetical pericentric inversion. In this regard, a compilation of 104 recombinant-like chromosomes of de novo or sporadic occurrence [Rivera et al., 2013] lists 11 other comparable chromosome-1 composites entailing dup q/del p but without an interstitial telomere. To avoid a nonsensical “der vs rec” controversy, we have designated such rearranged chromosomes with the official term rea coupled with the lengthy description of the novel composite [Rivera et al., 2013]. In that paper, we pointed out that “this formula makes no causal assumptions, unambiguously describes the rearranged chromosome, allows for a meiotic or mitotic origin, and is consistent with the involvement of 1 or 2 homologs”. Moreover, the term rea had already been used for this purpose [Thomas et al., 2006] and properly describes a rearranged unbalanced chromosome mimicking a recombinant ensued from a pericentric inversion as it is epitomized by the rea(1)(qter→q32::pter→qter) here alluded to. It goes without saying that inv dup is also improperly used to designate mirror structures such as isodicentrics and neocentric isofragments [e.g., Warburton et al., 2000]. Although Lévy et al. [2015] recognized that “[T]he recurrent nature of all these similar recombinants, including our dup(1q), suggests an identical mechanism of formation”, they failed to identify it. According to D’Angelo et al. [2009], who analyzed in fine detail two dup q/del p and two other comparable chromosome-1 rearrangements, the DNA repair mechanism of non-homologous end joining (NHEJ) appears to be “the pathway in the formation of these de novo nonreciprocal translocations, because of the lack of evidence to support a homology-based recombination mechanism”. Yet, the location in unique, non-repetitive DNA sequences of all the breakpoints in the four chromosome-1 rearrangements above mentioned [D’Angelo et al., 2009] may call into question the NHEJ mechanism for rearranged chromosomes with an interstitial telomere alike to the exceptional rea(1) documented by Lévy et al. [2015]. Because Lévy et al. [2015] also omitted some relevant references on other rearrangements with interstitial telomeres, I reiterate here the academic and moral duty that authors, reviewers, editors, and readers have to improve the current citation practices [Rivera, 2014]. Finally, I stress that seven months ago a Letter to the Editor with these comments was judged unacceptable by the concerned journal because “the conclusions of Dr. Levy's paper are really not about terminology and nomenclature”. REFERENCES D’Angelo CS, Gajecka M, Kim CA, Gentles AJ, Glotzbach CD, Shaffer LG, Koiffmann CP. 2009. Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements. Hum Genet 125:551-563. Lévy J, Receveur A, Jedraszak G, Chantot-Bastaraud S, Renaldo F, Gondry J, Andrieux J, Copin H, Siffroi J-P, Portnoï M-F. 2015. Involvement of interstitial telomeric sequences in two new cases of mosaicism for autosomal structural rearrangements. Am J Med Genet Part A 167A:428-433. Rivera H. Commentary: peer review and incomplete reference lists. 2014. Account Res 21:138-141. Rivera H, Domínguez MG, Vásquez-Velásquez AI, Lurie IW. 2013. De novo dup p/del q or dup q/del p rearranged chromosomes: review of 104 cases of a distinct chromosomal mutation. Cytogenet Genome Res 141: 58-63. Shaffer LG, McGowan-Jordan J, Schmid M. 2013. ISCN 2013: an international system for human cytogenetic nomenclature (2013), Basel, S Karger. p. 69. Thomas NS, Durkie M, Van Zyl B, Sanford R, Potts G, Youings S, Dennis N, Jacobs P. 2006. Parental and chromosomal origin of unbalanced de novo structural chromosome abnormalities in man. Hum Genet 119: 444-450. Warburton PE, Dolled M, Mahmood R, Alonso A, Li S, Naritomi K, Tohma T, Nagai T, Hasegawa T, Ohashi H, Govaerts LC, Eussen BH, Van Hemel JO, Lozzio C, Schwartz S, Dowhanick-Morrissette JJ, Spinner NB, Rivera H, Crolla JA, Yu C, Warburton D. 2000. Molecular cytogenetic analysis of eight inversion duplications of human chromosome 13q that each contain a neocentromere. Am J Hum Genet 66:1794-1806.

On 2015 Oct 22, Horacio Rivera commented:

A de novo inv dup(1) turns out to be a rea(1)dup q chromosome I remark that the de novo mosaic 1q32→qter duplication onto 1pter (concomitant with a normal clone) described by Levy et al. [2015] is not an inverted duplication because direct and inverted duplications are officially defined as “a gain of a chromosomal segment observed at the original chromosome location” [Shaffer et al., 2013], not to mention that the orientation of the extra segment was indeed a direct one. It is significant that in their discussion, Lévy et al. [2015] refer to three other similar chromosome-1 rearrangements entailing an 1q duplication (although none with interstitial telomeric repeats) and visualize them as “recombinants” from an hypothetical pericentric inversion. In this regard, a compilation of 104 recombinant-like chromosomes of de novo or sporadic occurrence [Rivera et al., 2013] lists 11 other comparable chromosome-1 composites entailing dup q/del p but without an interstitial telomere. To avoid a nonsensical “der vs rec” controversy, we have designated such rearranged chromosomes with the official term rea coupled with the lengthy description of the novel composite [Rivera et al., 2013]. In that paper, we pointed out that “this formula makes no causal assumptions, unambiguously describes the rearranged chromosome, allows for a meiotic or mitotic origin, and is consistent with the involvement of 1 or 2 homologs”. Moreover, the term rea had already been used for this purpose [Thomas et al., 2006] and properly describes a rearranged unbalanced chromosome mimicking a recombinant ensued from a pericentric inversion as it is epitomized by the rea(1)(qter→q32::pter→qter) here alluded to. It goes without saying that inv dup is also improperly used to designate mirror structures such as isodicentrics and neocentric isofragments [e.g., Warburton et al., 2000]. Although Lévy et al. [2015] recognized that “[T]he recurrent nature of all these similar recombinants, including our dup(1q), suggests an identical mechanism of formation”, they failed to identify it. According to D’Angelo et al. [2009], who analyzed in fine detail two dup q/del p and two other comparable chromosome-1 rearrangements, the DNA repair mechanism of non-homologous end joining (NHEJ) appears to be “the pathway in the formation of these de novo nonreciprocal translocations, because of the lack of evidence to support a homology-based recombination mechanism”. Yet, the location in unique, non-repetitive DNA sequences of all the breakpoints in the four chromosome-1 rearrangements above mentioned [D’Angelo et al., 2009] may call into question the NHEJ mechanism for rearranged chromosomes with an interstitial telomere alike to the exceptional rea(1) documented by Lévy et al. [2015]. Because Lévy et al. [2015] also omitted some relevant references on other rearrangements with interstitial telomeres, I reiterate here the academic and moral duty that authors, reviewers, editors, and readers have to improve the current citation practices [Rivera, 2014]. Finally, I stress that seven months ago a Letter to the Editor with these comments was judged unacceptable by the concerned journal because “the conclusions of Dr. Levy's paper are really not about terminology and nomenclature”. REFERENCES D’Angelo CS, Gajecka M, Kim CA, Gentles AJ, Glotzbach CD, Shaffer LG, Koiffmann CP. 2009. Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements. Hum Genet 125:551-563. Lévy J, Receveur A, Jedraszak G, Chantot-Bastaraud S, Renaldo F, Gondry J, Andrieux J, Copin H, Siffroi J-P, Portnoï M-F. 2015. Involvement of interstitial telomeric sequences in two new cases of mosaicism for autosomal structural rearrangements. Am J Med Genet Part A 167A:428-433. Rivera H. Commentary: peer review and incomplete reference lists. 2014. Account Res 21:138-141. Rivera H, Domínguez MG, Vásquez-Velásquez AI, Lurie IW. 2013. De novo dup p/del q or dup q/del p rearranged chromosomes: review of 104 cases of a distinct chromosomal mutation. Cytogenet Genome Res 141: 58-63. Shaffer LG, McGowan-Jordan J, Schmid M. 2013. ISCN 2013: an international system for human cytogenetic nomenclature (2013), Basel, S Karger. p. 69. Thomas NS, Durkie M, Van Zyl B, Sanford R, Potts G, Youings S, Dennis N, Jacobs P. 2006. Parental and chromosomal origin of unbalanced de novo structural chromosome abnormalities in man. Hum Genet 119: 444-450. Warburton PE, Dolled M, Mahmood R, Alonso A, Li S, Naritomi K, Tohma T, Nagai T, Hasegawa T, Ohashi H, Govaerts LC, Eussen BH, Van Hemel JO, Lozzio C, Schwartz S, Dowhanick-Morrissette JJ, Spinner NB, Rivera H, Crolla JA, Yu C, Warburton D. 2000. Molecular cytogenetic analysis of eight inversion duplications of human chromosome 13q that each contain a neocentromere. Am J Hum Genet 66:1794-1806.