Subtelomere specific microarray based comparative genomic hybridisation: a rapid detection system for cryptic rearrangements in idiopathic mental retardation

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Abstract
BAC/PAC clones used in this study are shown in table 1. We selected subtelomeric clones based on the second generation set of human chromosome specific subtelomeric probes reported by Knight et al.8 Five clones (GS-124I4 for 16p, GS-48O23 and GS-325I23 for 19q, GS-82O2 for 20p, and GS-202M24 for Xq) that showed signals appearing at sites different from those originally reported were excluded from this study. Three clones (GS-99K24, CITD-3018K1 for 22q, and GS-225F6 for XqYq) were unavailable. New clones (RP11-359B7 for 19q, RP11-238J15 for 20p, RP3-402G11 for 22q, and RP11-431N21 for XqYq) were obtained from online databases, the human telomere mapping and sequencing project (http://www.wistar.upenn.edu/Riethman/) and the human genome browser (http://genome.ucsc.edu/cgi-bin/hgGateway?Db=hg11). Although RP11-431N21 mapped to Xq/Yq showed unequal signal intensities between Xq and Yq (FISH signals of Xq were twice as intense as those of Yq), we included it in our microarray because no other suitable clones could be obtained. In addition, we added two X chromosome specific clones (RP11-267O9 on Xp22.32 and RP4-617A9 on Xp22.3) as internal controls. Clones were purchased from either Incyte Genomics (Polo Alto, CA, USA) or Invitrogen (Carlsbad, CA, USA). DNA was extracted using QIAgen Plasmid Midi kits (QIAgen, Hilden, Germany) from 200 ml bacterial culture with appropriate antibiotics according to the manufacturer’s protocol.

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