Nucleic Acids Research, 2003, Vol. 31, No. 16 e97
© 2003 Oxford University Press
Ligation of high-melting-temperature ‘clamp’ sequence extends the scanning range of rare point-mutational analysis by constant denaturant capillary electrophoresis (CDCE) to most of the human genome
Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
*To whom correspondence should be addressed at present address: Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. Mailstop C1-015 Seattle, WA 98109, USA. Tel: +1 206 667 4544; Fax: +1 206 667 5815; Email: akim{at}fhcrc.org
Mutations cause or influence the prevalence of many diseases. In human tissues, somatic point mutations have been observed at fractions at or below 4/10 000 and 5/100 000 in mitochondrial and nuclear DNA, respectively. In human populations, fractions for the multiple alleles that code for recessive deleterious syndromes are not expected to exceed 5 x 10–4. Both nuclear and mitochondrial point mutations have been measured in human cells and tissues at fractions approaching 10–6 using constant denaturant capillary electrophoresis (CDCE) coupled with high-fidelity PCR (hifiPCR). However, this approach is only applicable to those target sequences (
100 bp) juxtaposed with a ‘clamp’, a higher-melting-temperature sequence, in genomic DNA; such naturally clamped targets represent 9% of the human genome. To open up most of the human genome to rare point-mutational analysis, a high-efficiency DNA ligation procedure was recently developed so that a clamp could be attached to any target of interest. We coupled this ligation procedure with prior CDCE/hifiPCR and achieved a sensitivity of 2 x 10–5 in human cells for the first time using an externally attached clamp. At this sensitivity, somatic mutations, each representing an anatomically distinct cluster of cells (turnover unit) derived from a mutant stem cell, may be detected in a series of tissue samples, each containing as many as 5 x 104 turnover units. Additionally, rare inherited mutations may be scanned in pooled DNA samples, each derived from as many as 105 persons.