The lumpiness of the “CNVome” ! Why is it so? …and what does it tell us?

Greg B Peters1, Con Ngo, & Dale Wright.

1 Sydney Genome Diagnostics, Children’s Hospital Westmead, Hawkesbury Road & Hainsworth Street, Westmead, NSW 2145, Australia

 

Microarray technology has been in routine diagnostic use for more than a decade, and much data has been accumulated, concerning the size and distribution of those mutations classed as copy number variants [CNVs], across the human genome.  Elaborate maps of these distributions are now available, both in the large publicly-available databases, and in the many smaller databases accumulated in-house, by diagnostic laboratories like our own. From the total information embodied within these mappings, a clear understanding of CNV distribution should emerge.  It is a distribution that is strikingly non-random, heterogeneous, and peculiar.   And it is this entity we refer to here as the “CNVome”.

The CNVome in many places exhibits extreme clustering of its elements, some of this clustering associated with CNV length. The larger variants, for example, are often concentrated in analogous regions of each chromosome, e.g. the pericentric or sub-telomeric regions. To borrow a term from statistics and cosmology:  we might characterise the CNV distribution data as “lumpy” in its nature. And we might, on that basis, use that lumpiness to explore the origins [and fates] of the elements in question, to arrive at some model explaining their origin, incidence, and evolutionary persistence [not to mention their effects on their hosts: i.e. all of us]. Such a model is attempted here.

We further suggest that this lumpiness of the CNV data, and its potential explanatory power, has not yet received anything like the attention it deserves – possibly because:

  1. in our “post-genome” world, the dominant paradigm of DNA point mutation does not readily lend itself to an understanding of CNVs’ effects on fitness, and
  2. copy number mutation was traditionally the fiefdom of the cytogeneticists: an out-group considered extinct, from around the end of the Mesozoic.

Biography:

Greg Peters

PhD in the field of insect cytogenetics and population biology,  Australian National University (Canberra),1978.

FHGSA [Cytogenetics] 1991

FFSc(RCPA) 2010

HGSA State Secretary (South Australian Branch), 1986-8.

HGSA: Federal Treasurer, 1988-91.

Member of the assessment board for the ASOC* Cytogenetics QAP program, 1994-8.

Member of the assessment board for the ASOC/HGSA Microarray quality assessment program, 2009-2015.

Head of Cytogenetics, RNSH 1995-2000

Head of Cytogenetics, CHW 2000-2010

Introduced routine array testing from 2006.

Current:

Head of Microarray Testing,

Sydney Genome Diagnostics, Children’s Hospital at Westmead;

other appointment:

Conjoint Senior Lecturer, Discipline of Paediatrics and Child Health, Faculty of  Medicine, University of Sydney,

NSW, Australia.

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