Wong Lee-Jun C, Dimmock David, Geraghty Michael T, Quan Richard, Lichter-Konecki Uta, Wang Jing, Brundage Ellen K, Scaglia Fernando, Chinault A Craig
Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Clin Chem. 2008 Jul;54(7):1141-8. doi: 10.1373/clinchem.2008.103721. Epub 2008 May 16.
direct DNA sequencing is the primary clinical technique for identifying mutations in human disease, but sequencing often does not detect intragenic or whole-gene deletions. Oligonucleotide array-based comparative genomic hybridization (CGH) is currently in clinical use to detect major changes in chromosomal copy number.
a custom oligonucleotide-based microarray was constructed to provide high-density coverage of an initial set of 130 nuclear genes involved in the pathogenesis of metabolic and mitochondrial disorders. Standard array CGH procedures were used to test patient DNA samples for regions of copy number change. Sequencing of regions of predicted breakpoints in genomic DNA and PCR analysis were used to confirm oligonucleotide array CGH data.
oligonucleotide array CGH identified intragenic exonic deletions in 2 cases: a heterozygous single-exon deletion of 4.5 kb in the SLC25A13 gene [solute carrier family 25, member 13 (citrin)] in an individual with citrin deficiency and a homozygous 10.5-kb deletion of exons 13-17 in the ABCB11 gene [PFIC2, ATP-binding cassette, sub-family B (MDR/TAP), member 11] in a patient with progressive familial intrahepatic cholestasis. In 2 females with OTC deficiency, we also found 2 large heterozygous deletions of approximately 7.4 Mb and 9 Mb on the short arm of the X chromosome extending from sequences telomeric to the DMD gene [dystrophin (muscular dystrophy, Duchenne and Becker types)] to sequences within or centromeric to the OTC gene (ornithine carbamoyltransferase).
these examples illustrate the successful use of custom oligonucleotide arrays to detect either whole-gene deletions or intragenic exonic deletions. This technology may be particularly useful as a complementary diagnostic test in the context of a recessive disease when only one mutant allele is found by sequencing.
直接DNA测序是识别人类疾病突变的主要临床技术，但测序常常无法检测到基因内或全基因缺失。基于寡核苷酸阵列的比较基因组杂交（CGH）目前已应用于临床，用于检测染色体拷贝数的主要变化。
构建了一个基于定制寡核苷酸的微阵列，以对涉及代谢和线粒体疾病发病机制的最初130个核基因进行高密度覆盖。采用标准的阵列CGH程序检测患者DNA样本中拷贝数变化的区域。对基因组DNA中预测断点区域进行测序及PCR分析，以确认寡核苷酸阵列CGH数据。
寡核苷酸阵列CGH在2例中鉴定出基因内外显子缺失：1例柠檬酸转运蛋白缺乏症患者的SLC25A13基因[溶质载体家族25成员13（柠檬酸转运蛋白）]存在杂合性单外显子4.5 kb缺失；1例进行性家族性肝内胆汁淤积症患者的ABCB11基因[PFIC2，ATP结合盒亚家族B（MDR/TAP）成员11]存在纯合性10.5 kb外显子13 - 17缺失。在2例鸟氨酸氨基甲酰转移酶缺乏症女性患者中，我们还在X染色体短臂上发现了2个大约7.4 Mb和9 Mb的大的杂合性缺失，缺失区域从端粒到DMD基因[肌营养不良蛋白（杜兴氏和贝克氏型肌营养不良症）]的序列延伸至OTC基因（鸟氨酸氨基甲酰转移酶）内或着丝粒侧的序列。
这些实例说明了定制寡核苷酸阵列在检测全基因缺失或基因内外显子缺失方面的成功应用。在隐性疾病的情况下，当通过测序仅发现一个突变等位基因时，该技术作为一种补充诊断测试可能特别有用。
