ArticleBMC genomics2017
High resolution measurement of DUF1220 domain copy number from whole genome sequence data.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Understanding the Emergence of Schizophrenia in the Light of Human Evolution: New Perspectives in Genetics.Genes, brain, and behavior · 2025Review
- Article
- Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution.Nature reviews. Genetics · 2023Review
- Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution.Life science alliance · 2023Article
- Review
- Global Repeat Map (GRM): Advantageous Method for Discovery of Largest Higher-Order Repeats (HORs) in Neuroblastoma Breakpoint Family (NBPF) Genes, in Hornerin Exon and in Chromosome 21 Centromere.Progress in molecular and subcellular biology · 2021Article
- Disorders Associated With Diverse, Recurrent Deletions and Duplications at 1q21.1.Frontiers in genetics · 2020Article
- The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome.Genetics · 2020Article
- A Third Linear Association Between Olduvai (DUF1220) Copy Number and Severity of the Classic Symptoms of Inherited Autism.The American journal of psychiatry · 2019Article
- Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development.Genome biology and evolution · 2018Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundDUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid copies of DUF1220 in hg38 (~160 of which are human-specific) and the majority of these can be divided into 6 different subtypes (referred to as clades). Copy number changes of specific DUF1220 clades have been associated in a dose-dependent manner with brain size variation (both evolutionarily and within the human population), cognitive aptitude, autism severity, and schizophrenia severity. However, no published methods can directly measure copies of DUF1220 with high accuracy and no method can distinguish between domains within a clade.
resultsHere we describe a novel method for measuring copies of DUF1220 domains and the NBPF genes in which they are found from whole genome sequence data. We have characterized the effect that various sequencing and alignment parameters and strategies have on the accuracy and precision of the method and defined the parameters that lead to optimal DUF1220 copy number measurement and resolution. We show that copy number estimates obtained using our read depth approach are highly correlated with those generated by ddPCR for three representative DUF1220 clades. By simulation, we demonstrate that our method provides sufficient resolution to analyze DUF1220 copy number variation at three levels: (1) DUF1220 clade copy number within individual genes and groups of genes (gene-specific clade groups) (2) genome wide DUF1220 clade copies and (3) gene copy number for DUF1220-encoding genes.
conclusionsTo our knowledge, this is the first method to accurately measure copies of all six DUF1220 clades and the first method to provide gene specific resolution of these clades. This allows one to discriminate among the ~300 haploid human DUF1220 copies to an extent not possible with any other method. The result is a greatly enhanced capability to analyze the role that these sequences play in human variation and disease.
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