新しい全ゲノム解析:Charcot–Marie–Tooth病

whole genome sequencing studyは、特異的であり、臨床的に明らかな遺伝子変異同定に役立つことが、Charcot-Marie-Tooth (CMT) neuropathyで明らかとなった。

ヒューストンのBaylor College of Medicineの Department of Molecular and Human Geneticsの研究者らが、次世代sequencing methodを用いて報告したもの
PMP22, MPZ, PRX, GDAP1, EGR2といった遺伝子を含む変異に関係していたことで、このテクニックにより、探し求めるものが正確でなくても見いだされる可能性と、多くの考察に寄与する知見を見いだすこととなるだろうと述べている。


Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy
N Engl. J Med. Vol. 362:(13) 1181-1191 Apr. 1, 2010


疾患の遺伝子診断は異種遺伝子の検討は、Charcot–Marie–Tooth disease などのような場合に用いられる。全ゲノム配列研究で、 SH3TC2 (the SH3 domain and tetratricopeptide repeats 2 gene)が複合的、heterozygous、原因的遺伝子で、いくつかのsubclinicalな発現型が2つの遺伝子変異独立して関連し、故にcarpal tunnel syndromeを含むニューロパチーに影響を与えることが明確となった。

DNA配列や変異の遺伝子特異的解析により予後情報、リスクに関する遺伝子コンサルトなどがなされている。cystic fibrosis1 などの常染色体劣性やneurofibromatosis type 12などの優性遺伝では、単一遺伝子の役割が明らか。しかし多くのメンデル性疾患の発現型は遺伝的に異種遺伝子型であり、原因となる変異は難聴や retinitis pigmentosaで、100を超すほど同定されている。
さらに特異的変異が、優性、劣性、digenic、triallelicな特性など分かれる発現型も多い。
メンデル性疾患に影響を与えるmodifying lociに関して、強固なエビデンスが存在する。
特性がよく知られた病的経過を有する症候群の単純な遺伝子パターンでさえ、個々の家族内では複雑であることがある。

Charcot–Marie–Tooth disease は、2つの病型をもつ、遺伝性の末梢神経性疾患
・ demyelinating form (type 1) affecting the glia-derived myelin
・axonal form (type 2) affecting the nerve axon
これは、電気生理的、神経病態的検査により鑑別が行われる

Charcot–Marie–Tooth disease は、遺伝子heterogeneityに関するモデル疾患として用いられ
臨床的重傷度の遺伝子パターン、主要遺伝子と修正遺伝子の重要性が検討されている。

Charcot–Marie–Tooth diseaseの変異対立遺伝子は、常染色体性、劣性で、X連鎖性で、39の分離したlocusのSNPsとコピー数変異も認められ、疾患の成りやすさに関連する
疾患の成りやすさに関する変異は主に優性遺伝であるが、locus 14の遺伝子は劣性である。
成人発症、 Charcot–Marie–Tooth diseaseは、発現にばらつきが多いが、distal symmetrical neuropathyとして特徴付けられ、緩徐進行性の筋力低下と萎縮(特に腓骨部位の筋萎縮が著明)として特徴付けられている結果、背屈筋力低下、下垂足、2次性の鶏歩(steppage gait)を生じる。Pes cavus (凹足、特にhighly arched feet) や pes planus (扁平足:flat feet)が多くの患者で見られる。

この報告では次世代sequencing methodで、遺伝性のニューロパチー家系の原因調査を行い、通常のコモンなCharcot–Marie–Tooth 遺伝子、PMP、 MPZ、 PRX、GDAP1、 EGR2を含む遺伝子の変化からネガティブであった対象者を検討





Glossary

・Array-based comparative genomic hybridization: A hybridization method for detecting copy-number variations in DNA samples from a patient as compared with a control sample. The method provides higher resolution than cytogenetic methods but lower resolution than sequencing methods.

・Average depth of coverage: The average number of times each base in the genome was sequenced, as a function of the distribution and number of sequence reads that map to the reference genome.

・Coding single-nucleotide polymorphisms: Single DNA-base changes that occur in the coding regions of genes.

・Copy-number variation: DNA changes that involve sequences of more than 100 bp, larger than single-nucleotide changes or microsatellites, and that vary in their number of copies among individual persons. These variants can be benign and polymorphic, but some can cause disease.

・DNA template: An individual fragment of DNA that is available for sequencing.

・Exon capture: Methods for isolating and sequencing gene exons, to the exclusion of the remainder of the genome. The DNA templates from exons are "captured" with the use of probes complementary to the targeted exon sequences. After capture, the targeted DNA is eluted and sequenced. The cost of exon capture can be 10 to 50% lower than that of whole-genome sequencing, although the method is insensitive to copy-number variations and mutations that are outside the targeted regions.

・Fragment-sequence read: The contiguous nucleotide sequence from one end of a DNA template (as opposed to a mate-pair read).

・Haploinsufficiency: The state that occurs when a diploid organism has only a single functional copy of a gene, which does not produce enough protein to support normal function.

・Mapping: The computational process of identifying the specific region of a reference genome from which an individual sequenced DNA template originated.

・Mappable yield: The number of bases generated by a DNA-sequencing instrument that can be mapped to the reference genome.

・Mate-pair sequencing: A sequencing strategy that permits the inference of structural changes in a genome by sequencing at both the 5' and 3' ends of each DNA template (as opposed to the fragment-sequencing approach).

・Mendelian disease: Human disease caused by mutations in a single gene.

・Missense mutations: Single DNA-base changes that occur in the coding regions of genes and alter the resulting encoded amino acid sequence.

・Next-generation sequencing: DNA-sequencing methods that involve chemical assays other than the traditional Sanger dideoxy-chain-termination method. Next-generation-sequencing methods produce much larger quantities of data at less expense, but the individual raw sequence reads that are generated from individual amplified DNA-template sequences are shorter and have lower quality.

・Nonsense mutations: DNA-base changes that introduce termination codons in the coding sequences of genes, resulting in truncated proteins.

・Sequence read: The sequence generated from a single DNA template.

・Single-base error rate: The total number of mismatched bases found in mapped sequence reads from a sequencing run, divided by the mappable yield. This rate estimates the probability that any given mappable base is an error.

・Two-base encoding: A method used in the SOLiD (Sequencing by Oligonucleotide Ligation and Detection) DNA-sequencing platform that represents a DNA sequence as a chain of overlapping dimers encoded as single-base "colors." This allows for sequencing of the 16 unique sequence dimers with the use of only four unique dye colors and provides a method for improving the overall accuracy of the sequence reads (reducing the single-base error rate).

by internalmedicine | 2010-04-01 10:53 | 中枢神経  

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