High resolution measurement of DUF1220 domain copy number from whole genome sequence data

Astling, David P.; Heft, Ilea; Jones, Kenneth L.; Sikela, James M.

doi:10.1186/s12864-017-3976-z

Cited by 16 publications

(17 citation statements)

References 40 publications

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“…However, this gene and its role in human diseases have not been curated in OMIM. DUF1220 sequences predominantly exist in neuroblastoma breakpoint family (NBPF) genes (Astling et al, 2017). By applying specialized bioinformatics tools for analyzing the CNVs of DUF1220 from 42 patients with either the 1q21.1 deletion or the reciprocal duplications, Dumas et al (2012) proposed that the DUF1220 sequences in the NBPF genes were associated with brain size anomalies (Figure 4).…”

Section: Discussionmentioning

confidence: 99%

Disorders Associated With Diverse, Recurrent Deletions and Duplications at 1q21.1

Hui

Kim

et al. 2020

Front. Genet.

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The subchromosomal region 1q21.1 is one of the hotspots in the human genome for deletions and reciprocal duplications, owing to the existence of hundreds of segmental duplications. Recurrent deletions and duplications in this region are thought to be causative in patients with variable clinical manifestations. Based on the genomic locations, deletions and duplications at the 1q21.1 locus have been associated with distinguishable syndromes: chromosome 1q21.1 deletion syndrome, chromosome 1q21.1 duplication syndrome, and thrombocytopenia-absent radius (TAR) syndrome, which is partially due to deletions at the proximal 1q21.1 region. We report here diverse, recurrent deletions and duplications at the 1q21.1 locus in 36 patients from a cohort of 5,200 individuals. Among the 36 patients, 18 patients carry 1q21.1 deletions, nine individuals have reciprocal duplications at 1q21.1, two patients share an identical short deletion, and the remaining seven possess variable sizes of duplications at the proximal 1q21.1 region. Furthermore, we provide cytogenetic characterization and detailed clinical features for each patient. Notably, duplications at the proximal 1q21.1 region have not been associated with a defined disorder in publications. However, recurrent duplications at the proximal 1q21.1 region among the seven patients strongly suggested that the variants are likely pathogenic. The common phenotypical features of those disorders are also summarized to facilitate clinical diagnoses and genetic counseling.

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Section: Discussionmentioning

confidence: 99%

Disorders Associated With Diverse, Recurrent Deletions and Duplications at 1q21.1

Hui

Kim

et al. 2020

Front. Genet.

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“…Concomitant with the increase in the number of NBPF genes in the human lineage, a striking increase in the copy number of this domain was observed [ 84 ]. Moreover, a high number of copies of this domain has been found to be correlated with brain size and the severity of autism, whereas a low number of copies has been found to be correlated with the severity of schizophrenia [ 81 , 85 ]. Functional studies showed that overexpression of NBPF15 , which contains multiple copies of this domain, can increase the number of neural stem cells that can be generated from human embryonic stem cells [ 86 ].…”

Section: Other Human-specific Genes Expressed During Fetal Human Brain Developmentmentioning

confidence: 99%

Human-Specific Genes, Cortical Progenitor Cells, and Microcephaly

Heide

Huttner

2021

Cells

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Over the past few years, human-specific genes have received increasing attention as potential major contributors responsible for the 3-fold difference in brain size between human and chimpanzee. Accordingly, mutations affecting these genes may lead to a reduction in human brain size and therefore, may cause or contribute to microcephaly. In this review, we will concentrate, within the brain, on the cerebral cortex, the seat of our higher cognitive abilities, and focus on the human-specific gene ARHGAP11B and on the gene family comprising the three human-specific genes NOTCH2NLA, -B, and -C. These genes are thought to have significantly contributed to the expansion of the cerebral cortex during human evolution. We will summarize the evolution of these genes, as well as their expression and functional role during human cortical development, and discuss their potential relevance for microcephaly. Furthermore, we will give an overview of other human-specific genes that are expressed during fetal human cortical development. We will discuss the potential involvement of these genes in microcephaly and how these genes could be studied functionally to identify a possible role in microcephaly.

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“…The gene family neuroblastoma breakpoint family ( NBPF ) is characterized by domain of unknown function (DUF1220) protein domains that underwent the largest, >300, copy number expansion in humans ( Vandepoele et al 2005 ; Dumas and Sikela 2009 ; Sudmant et al 2010 , 2013 ; O’Bleness et al 2012a , 2012b ; Keeney et al 2014 ; Zimmer and Montgomery 2015 ; Astling et al 2017 ). This human-specific tandem repeat expansion was first described in 2006 ( Popesco et al 2006 ).…”

Section: Human-specific Segmental Duplications Deletions and Other mentioning

confidence: 99%

Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development

Levchenko

Kanapin

Samsonova

et al. 2017

Genome Biology and Evolution

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The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens, but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefrontal cortex. Human-specific deletions may remove regulatory sequences, such as enhancers. Segmental duplications, because of their large size, create new coding sequences, like new functional paralogs. Further functional study of these variants will shed light on evolution of our species, as well as on the etiology of neurodevelopmental disorders.

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High resolution measurement of DUF1220 domain copy number from whole genome sequence data

Cited by 16 publications

References 40 publications

Disorders Associated With Diverse, Recurrent Deletions and Duplications at 1q21.1

Disorders Associated With Diverse, Recurrent Deletions and Duplications at 1q21.1

Human-Specific Genes, Cortical Progenitor Cells, and Microcephaly

Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development

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