Figure S4 from Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer
Natali GulbahceMark Jesus M. MagbanuaRobert ChinMisha R. AgarwalXuhao LuoJia LiuDaniel M. HaydenQing MaoSerban CiotlosZhenyu LiYanxiang ChenXingpeng ChenYuxiang LiRebecca Yu ZhangKatharine LeeRick TearleEmily ParkSnezana DrmanacHope S. RugoJohn W. ParkRadoje DrmanacBrock A. Peters
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<p>Copy number analysis based on read coverage in all batches. Read data is plotted starting from Chr1 and ending at ChrX. Each sample is labeled on the right side of the plot. All CTC samples identify chr1q amplification, and chr13 and chr16q losses.</p>Keywords:
Cancer Therapy
Sample (material)
Hybrid genome assembly
Sequence assembly
Multiplex
Cancer genome sequencing
Illumina dye sequencing
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Sequencing whole plant genomes has advanced rapidly with the development of next generation sequencing (NGS) technologies and bioinformatics, enabling the study of large and complex genomes such as that of the hexaploid cereal, Triticum aestivum L. (bread wheat). Despite advances, however, confounding factors such as repetitive elements and low polymorphism still hinder sequencing attempts. Isolation techniques such as sequencing of diploid progenitors and chromosome separation through flow cytometry have showed promise in reducing the size of the genome for sequencing. In this review we discuss the advances and stumbling blocks that have been encountered on the road toward the complete hexaploid wheat genome sequence. We also discuss the latest complimentary techniques and the progression of accumulation of sequence data relevant to wheat genome research.
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5개 Populus수종(은백양, 수원사시, 현사시, 은사시, 미루나무)으로부터 DNA를 추출, 이들 DNA의 재결합 kinetics를 분석하여 DNA 반복구조의 양 반복 unit의 길이, 반복횟수를 측정한 결과 5개 Populus수종의 genome구조는 10,000 NTP 이상의 long-repetivtive DNA sequence가 길이가 서로 다른 single copy sequence 사이에 중빈도 반복(은사시), 또는 고빈도 반복(은백양, 수원사시, 현사시., 미루나무)의 long-period interspersion pattern으로 분산 배치되어 있는 것으로 나타났다.
또한 각 DNA의 melting temperature로부터 G+C content를 산출한 결과 5개 수종 사이에 뚜렷한 어떤 경향은 보이지 않았으나 현사시와 은사시의 경우 G+C content가 각각 48.1%, 56.6%로 큰 차이를 나타내어 이를 genome구조와 연관시켜 볼 때 이들 두 수종의 genome구조는 차이가 있는 것으로 생각된다.
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The immune North American grapevine species Vitis rotundifolia Michaux (subgen. Muscadinia Planch.) is regarded as a potential donor of disease resistance genes, withstanding such dangerous diseases of grapes as powdery and downy mildews. The cultivar ‘Dixie’ is the only representative of this species preserved ex situ in Russia: it is maintained by the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) in the orchards of its branch, Krymsk Experiment Breeding Station. Third-generation sequencing on the MinION platform was performed to obtain information on the primary structure of the cultivar’s genomic DNA, employing also the results of Illumina sequencing available in databases. A detailed description of the technique with modifications at various stages is presented, as it was used for grapevine genome sequencing and whole-genome sequence assembly. The modified technique included the main stages of the original protocol recommended by the MinION producer: 1) DNA extraction; 2) preparation of libraries for sequencing; 3) MinION sequencing and bioinformatic data processing; 4) de novo whole-genome sequence assembly using only MinION data or hybrid assembly (MinION+Illumina data); and 5) functional annotation of the whole-genome assembly. Stage 4 included not only de novo sequencing, but also the analysis of the available bioinformatic data, thus minimizing errors and increasing precision during the assembly of the studied genome. The DNA isolated from the leaves of cv. ‘Dixie’ was sequenced using two MinION flow cells (R9.4.1).
Minion
Illumina dye sequencing
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ABSTRACT The sequence of the genome of “ Candidatus Tremblaya princeps” strain PCVAL, the primary endosymbiont of the citrus mealybug Planococcus citri , has been determined. “ Ca . Tremblaya princeps” presents an unusual nested endosymbiosis and harbors a gammaproteobacterial symbiont within its cytoplasm in all analyzed mealybugs. The genome sequence reveals that “ Ca . Tremblaya princeps” cannot be considered an independent organism but that the consortium with its gammaproteobacterial symbiotic associate represents a new composite living being.
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Hybrid genome assembly
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Cancer genome sequencing
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Lactobacillus reuteri, inhabiting the gastrointestinal tracts of a range of vertebrates, is a true symbiont with effects established as beneficial to the host. Here we describe the draft genome of L. reuteri ATCC 53608, isolated from a pig. The genome sequence provides important insights into the evolutionary changes underlying host specialization.
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Sequence (biology)
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Genome sequencing has become one of the most rapid and effective methods to study molecular breeding of animals and plants. Chickens and chicken products are the necessary production for people and play an important role in our lives. Chickens are the first species of birds to get the whole genome sequence. This paper reviewed the research situation of domestic chicken reference genome and whole genome sequencing, which revealed the selective genes of special traits of local chicken breeds. It is believed that with the development of science and technology, whole genome sequencing combined with data from other sources can continuously promote the progress of this discipline.
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Sanger sequencing
Cancer genome sequencing
Personal genomics
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The photoautotrophic cyanobacterium Synechocystis sp. PCC 6803 is a widely used model in genomic research and was the first photosynthetic organism to have its entire genome sequenced. Here, we report the genome sequence for two glucose-tolerant laboratory ‘wild-type’ strains, GT-O1 and GT-O2, in use at the University of Otago. Using high-throughput genome sequencing techniques and subsequent Sanger sequencing of detected variants, we have identified ten de novo mutations in the two strains, of which six are unique to GT-O2 cells. The presence of these unique mutations highlights the need to know the genomic background of the parent strain when constructing mutants in Synechocystis sp. PCC 6803 strains.
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