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1. Full Text Genotyping‐in‐Thousands by sequencing (GT‐seq): A cost effective SNP genotyping method based on custom amplicon sequencing
by Campbell, Nathan R and Harmon, Stephanie A and Narum, Shawn R
Molecular Ecology Resources, ISSN 1755-098X, 07/2015, Volume 15, Issue 4, pp. 855 - 867
Genotyping‐in‐Thousands by sequencing ( GT ‐seq) is a method that uses next‐generation sequencing of multiplexed PCR products to generate genotypes from... 
genotyping by sequencing | amplicon sequencing | SNP | seq | next‐generation sequencing | GT-seq | Next-generation sequencing | Amplicon sequencing | Genotyping by sequencing | EVOLUTIONARY BIOLOGY | CONSERVATION | next-generation sequencing | BIOCHEMISTRY & MOLECULAR BIOLOGY | MARKERS | ECOLOGY | DISCOVERY | High-Throughput Nucleotide Sequencing - economics | Computational Biology - methods | Animals | Cost-Benefit Analysis | Genotyping Techniques - economics | Oncorhynchus mykiss - classification | Oncorhynchus mykiss - genetics | Polymorphism, Single Nucleotide | Genotyping Techniques - methods | High-Throughput Nucleotide Sequencing - methods | Computational Biology - economics | Analysis | Methods | Single nucleotide polymorphisms | Fish | Libraries | Polymorphism | Index Medicus
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2. Full Text The Interlaboratory RObustness of Next-generation sequencing (IRON) study: a deep sequencing investigation of TET2, CBL and KRAS mutations by an international consortium involving 10 laboratories
by Kohlmann, A and Klein, H.U and Weissmann, S and Bresolin, S and Chaplin, T and Cuppens, H and Haschke-Becher, E and Garicochea, B and Grossmann, V and Hanczaruk, B and Hebestreit, K and Gabriel, C and Iacobucci, I and Jansen, J.H and Kronnie, G. Te and Locht, L.T. van de and Martinelli, G and McGowan, K and Schweiger, M.R and Timmermann, B and Vandenberghe, P and Young, B.D and Dugas, M and Haferlach, T
Leukemia, ISSN 0887-6924, 2011, Volume 25, Issue 12, pp. 1840 - 1848
Massively parallel pyrosequencing allows sensitive deep sequencing to detect molecular aberrations. Thus far, data are limited on the technical performance in... 
coverage | amplicon | 454 | deep sequencing | next-generation sequencing | mutation analysis | RAS | GENE | ONCOLOGY | HIGH-RESOLUTION | MYELOID-LEUKEMIA | HEMATOLOGY | CLONES | CHRONIC MYELOMONOCYTIC LEUKEMIA | REVEALS | Proto-Oncogene Proteins c-cbl - genetics | ras Proteins - genetics | Proto-Oncogene Proteins p21(ras) | Prognosis | Humans | Leukemia, Myelomonocytic, Chronic - genetics | Middle Aged | Male | Proto-Oncogene Proteins - genetics | DNA-Binding Proteins - genetics | Mutation - genetics | DNA Mutational Analysis | Polymerase Chain Reaction | Aged, 80 and over | Female | Aged | High-Throughput Nucleotide Sequencing | Cohort Studies | Nucleotide sequence | Gene mutations | Physiological aspects | Genetic aspects | Research | Diagnosis | Myeloproliferative disorders | Index Medicus
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3. Full Text High-Throughput Genomic Data in Systematics and Phylogenetics
by Emily Moriarty Lemmon and Alan R. Lemmon
Annual Review of Ecology, Evolution, and Systematics, ISSN 1543-592X, 1/2013, Volume 44, Issue 1, pp. 99 - 121
High-throughput genomic sequencing is rapidly changing the field of phylogenetics by decreasing the cost and increasing the quantity and rate of data... 
Polymerase chain reaction | Biological taxonomies | Taxa | Genomics in Ecology, Evolution and Ststematics Theme | Genomics | Phylogenetics | Genetic loci | Genomes | Phylogeny | Sequencing | Hybridity | Genomic partitioning | Hybrid enrichment | Targeted amplicon sequencing | High-throughput sequencing | Model selection | Locus selection | Transcriptome sequencing | Anchored phylogenomics | RAD sequencing | Next-generation sequencing | Ultraconserved element enrichment | Phylogeny estimation | Target enrichment | Phylogenomics | EUKARYOTIC GENOMES | ULTRACONSERVED ELEMENTS | ENRICHMENT STRATEGIES | transcriptome sequencing | targeted amplicon sequencing | phylogenomics | ultraconserved element enrichment | phylogeny estimation | MAXIMUM-LIKELIHOOD | next-generation sequencing | POPULATION GENOMICS | hybrid enrichment | anchored phylogenomics | model selection | MULTIPLE SEQUENCE ALIGNMENTS | ESTIMATING SPECIES TREES | locus selection | GENE TREES | EVOLUTIONARY BIOLOGY | BAYESIAN PHYLOGENETICS | target enrichment | ECOLOGY | genomic partitioning | high-throughput sequencing | Research | Nucleotide sequencing | DNA sequencing | Data analysis | Accuracy | Comparative analysis
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4. Full Text Error filtering, pair assembly and error correction for next-generation sequencing reads
by Edgar, Robert C and Flyvbjerg, Henrik
Bioinformatics, ISSN 1367-4803, 12/2014, Volume 31, Issue 21, pp. 3476 - 3482
Motivation: Next-generation sequencing produces vast amounts of data with errors that are difficult to distinguish from true biological variation when coverage... 
AMPLICON READS | ILLUMINA | DIVERSITY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | High-Throughput Nucleotide Sequencing - methods | Software | Algorithms | Index Medicus | Filtration | Filtering | Mathematical analysis | Packages | Error correction | Sequencing | Bioinformatics | Assembly
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5. Full Text Reproducibility and quantitation of amplicon sequencing-based detection
by Zhou, Jizhong and Wu, Liyou and Deng, Ye and Zhi, Xiaoyang and Jiang, Yi-Huei and Tu, Qichao and Xie, Jianping and Van Nostrand, Joy D and He, Zhili and Yang, Yunfeng
The ISME Journal, ISSN 1751-7362, 08/2011, Volume 5, Issue 8, pp. 1303 - 1313
To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of... 
pyrosequencing | random sampling | amplicon sequencing | metagenomics | quantitation | reproducibility | AMPLIFICATION | METAGENOMICS | BACTERIAL DIVERSITY | GENES | SPECIES RICHNESS | SOIL | ECOLOGY | MICROBIAL COMMUNITY COMPOSITION | RARE BIOSPHERE | PCR | REVEALS | Shewanella - isolation & purification | DNA, Bacterial - genetics | Climate Change | Shewanella - genetics | Soil Microbiology | Oklahoma | Metagenomics - methods | RNA, Ribosomal, 16S - genetics | Sequence Analysis, DNA - methods | Index Medicus | Original
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6. Full Text Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing
by Lange, Vinzenz and Böhme, Irina and Hofmann, Jan and Lang, Kathrin and Sauter, Jürgen and Schöne, Bianca and Paul, Patrick and Albrecht, Viviane and Andreas, Johanna M and Baier, Daniel M and Nething, Jochen and Ehninger, Ulf and Schwarzelt, Carmen and Pingel, Julia and Ehninger, Gerhard and Schmidt, Alexander H
BMC Genomics, ISSN 1471-2164, 01/2014, Volume 15, Issue 1, pp. 63 - 63
Background: A close match of the HLA alleles between donor and recipient is an important prerequisite for successful unrelated hematopoietic stem cell... 
Dual indexing | Amplicon-based sequencing | Illumina MiSeq | 4-primer approach | HLA typing | Human leukocyte antigen | Fluidigm Access Array | NGS | SYSTEM | CELL TRANSPLANTATION | DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | HIGH-RESOLUTION | GENETICS & HEREDITY | Microfluidic Analytical Techniques | DNA - isolation & purification | DNA - analysis | Exons | Humans | Alleles | Polymerase Chain Reaction | DNA Primers - metabolism | Histocompatibility Testing - economics | HLA Antigens - genetics | Sequence Analysis, DNA | Histocompatibility Testing - instrumentation | Usage | Equipment and supplies | DNA sequencers | Histocompatibility testing | Methods | Economic aspects | Pumping machinery industry | Nucleotide sequencing | Analysis | DNA sequencing | Data analysis | Genes | Deoxyribonucleic acid--DNA | Stem cells | Index Medicus | Data processing
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7. Full Text Multiplex PCR targeted amplicon sequencing (MTA-Seq): Simple, flexible, and versatile SNP genotyping by highly multiplexed PCR amplicon sequencing
by Onda, Yoshihiko and Takahagi, Kotaro and Shimizu, Minami and Inoue, Komaki and Mochida, Keiichi
Frontiers in Plant Science, ISSN 1664-462X, 03/2018, Volume 9, pp. 201 - 201
Next-generation sequencing (NGS) technologies have enabled genome re-sequencing for exploring genome-wide polymorphisms among individuals, as well as targeted... 
Amplicon sequence | Marker panel | Genotyping | SNP | Natural accession | Brachypodium distachyon | natural accession | CUSTOM AMPLISEQ | MODEL SYSTEM | LOCAL ADAPTATION | INBRED LINES | genotyping | DISCOVERY | amplicon sequence | PLANT SCIENCES | GENETIC DIVERSITY | GENOMICS | marker panel | GRASS BRACHYPODIUM-DISTACHYON | DNA | GENERATION | Genomics | Genetic polymorphisms
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8. Full Text Ultra‐deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata)
by Lighten, Jackie and Oosterhout, Cock and Paterson, Ian G and McMullan, Mark and Bentzen, Paul
Molecular Ecology Resources, ISSN 1755-098X, 07/2014, Volume 14, Issue 4, pp. 753 - 767
We address the bioinformatic issue of accurately separating amplified genes of the major histocompatibility complex ( MHC ) from artefacts generated during... 
guppy | amplicon | major histocompatibility complex | copy number variation | multigene family | next‐generation sequencing | Multigene family | Copy number variation | Major histocompatibility complex | Next-generation sequencing | Amplicon | Guppy | SYSTEM | RECOMBINATION | next-generation sequencing | BIOCHEMISTRY & MOLECULAR BIOLOGY | MOLECULES | EVOLUTIONARY BIOLOGY | EVOLUTION | GENES | VERTEBRATES | ECOLOGY | DIVERSITY | SELECTION | Multigene Family | Reproducibility of Results | Animals | Poecilia - genetics | Alleles | Molecular Sequence Data | Gene Dosage | High-Throughput Nucleotide Sequencing | Histocompatibility Antigens Class II - genetics | Genotyping Techniques - methods | Allelomorphism | Nucleotide sequencing | Analysis | DNA sequencing | Index Medicus
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9. Full Text 2.7 million samples genotyped for HLA by next generation sequencing: Lessons learned
by Schöfl, Gerhard and Schöfl, Gerhard and Lang, Kathrin and Lang, Kathrin and Quenzel, Philipp and Quenzel, Philipp and Böhme, Irina and Böhme, Irina and Sauter, Jürgen and Sauter, Jürgen and Hofmann, Jan A and Hofmann, Jan A and Pingel, Julia and Pingel, Julia and Schmidt, Alexander H and Schmidt, Alexander H and Lange, Vinzenz and Lange, Vinzenz
BMC Genomics, ISSN 1471-2164, 02/2017, Volume 18, Issue 1, pp. 161 - 161
Background: At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-highvolume high-resolution genotyping of HLA loci for the... 
High throughput | HLA genotyping | High resolution | Novel alleles | Amplicon PCR | Primer dimers | PCR chimerism | DKMS | Next generation sequencing | NUMBER | HIGH-THROUGHPUT | POLYMERASE | LOCI | IMPACT | IMMUNOGENETICS | DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | HIGH-RESOLUTION | GENETICS & HEREDITY | PCR-MEDIATED RECOMBINATION | STEM-CELL TRANSPLANTATION | Computational Biology - methods | Humans | Alleles | Genotype | High-Throughput Nucleotide Sequencing | HLA Antigens - genetics | Genotyping Techniques | Sequence Analysis, DNA | Polymerase chain reaction | Usage | Histocompatibility antigens | HLA histocompatibility antigens | Research | High-throughput screening (Biochemical assaying) | Index Medicus
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10. Full Text Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis
by Wu, Liyou and Wen, Chongqing and Qin, Yujia and Yin, Huaqun and Tu, Qichao and Van Nostrand, Joy D and Yuan, Tong and Yuan, Menting and Deng, Ye and Zhou, Jizhong
BMC Microbiology, ISSN 1471-2180, 06/2015, Volume 15, Issue 1, pp. 125 - 125
Background: Although high-throughput sequencing, such as Illumina-based technologies (e.g. MiSeq), has revolutionized microbial ecology, adaptation of amplicon... 
Illumina Miseq | Amplicon sequencing | Microbial ecology | Phasing primer | Low diversity sample | Next generation sequencing | Microbial community | PATTERNS | MICROBIOLOGY | GENERATION | DIVERSITY | CARBON-DIOXIDE | DEPTH | DNA, Ribosomal - analysis | Humans | DNA Primers | Archaea - classification | Bacteria - genetics | Environmental Microbiology | Bacteria - classification | Saliva - microbiology | DNA, Bacterial - analysis | Archaea - genetics | DNA, Archaeal - analysis | High-Throughput Nucleotide Sequencing - methods | Sequence Analysis, DNA - methods | Biotechnology | Evaluation | Ribosomal RNA | Analysis | Ecosystems | Index Medicus
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11. Full Text Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing
by Ranjan, Ravi and Rani, Asha and Metwally, Ahmed and McGee, Halvor S and Perkins, David L
Biochemical and Biophysical Research Communications, ISSN 0006-291X, 01/2016, Volume 469, Issue 4, pp. 967 - 977
The human microbiome has emerged as a major player in regulating human health and disease. Translational studies of the microbiome have the potential to... 
16S rRNA | Metagenomics | Microbiota | Whole genome shotgun sequencing | Next-generation sequencing | Amplicon sequencing | Microbiome | BIOCHEMISTRY & MOLECULAR BIOLOGY | METAGENOMIC SEQUENCES | TRANSPLANTATION | HUMAN GUT MICROBIOME | THERAPY | CATALOG | BIOPHYSICS | DISEASE | HEALTH | TOOLS | AGE | Reproducibility of Results | Humans | Molecular Sequence Data | Bacteria - genetics | Bacteria - isolation & purification | Metagenome - genetics | DNA, Bacterial - genetics | Microbiota - genetics | Base Sequence | Chromosome Mapping - methods | Sensitivity and Specificity | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Sequence Analysis, DNA - methods | Genetic research | Microbiota (Symbiotic organisms) | RNA | Analysis | Genomics | Index Medicus
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12. Full Text Testing genotyping strategies for ultra‐deep sequencing of a co‐amplifying gene family: MHC class I in a passerine bird
by Biedrzycka, Aleksandra and Sebastian, Alvaro and Migalska, Magdalena and Westerdahl, Helena and Radwan, Jacek and MEMEG and Lund University and Lunds universitet
Molecular Ecology Resources, ISSN 1755-098X, 07/2017, Volume 17, Issue 4, pp. 642 - 655
Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co‐amplify, has until... 
amplicon sequencing | copy number variation | next‐generation sequencing | passerine MHC | bioinformatics | next-generation sequencing | SYSTEM | NUMBER | BIOCHEMISTRY & MOLECULAR BIOLOGY | LOCI | MAJOR HISTOCOMPATIBILITY COMPLEX | POLYMORPHISM | GUPPY POECILIA-RETICULATA | EVOLUTIONARY BIOLOGY | EVOLUTION | VERTEBRATES | ECOLOGY | DIVERSITY | SELECTION | Reproducibility of Results | Animals | Passeriformes - genetics | Genes, MHC Class I | High-Throughput Nucleotide Sequencing | Genotyping Techniques | Sequence Analysis, DNA | Genetic research | Nucleotide sequencing | Genes | DNA sequencing | Gene families | Gene sequencing | Amplification | Major histocompatibility complex | Genotyping | Reproducibility | Reliability analysis | Gene duplication | Jumping | Low frequencies | Histocompatibility | Genotypes | Index Medicus | Genetik | Biological Sciences | Copy number variation | Next-generation sequencing | Naturvetenskap | Amplicon sequencing | Passerine MHC | Genetics | Biologi | Natural Sciences | Bioinformatics
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