Random Insertional–Deletional Strand Exchange Mutagenesis (RAISE): A Simple Method for Generating Random Insertion and Deletion Mutations

2014 ◽  
pp. 151-158 ◽  
Author(s):  
Ryota Fujii ◽  
Motomitsu Kitaoka ◽  
Kiyoshi Hayashi
Keyword(s):  
Strand Exchange ◽  
Simple Method ◽  
Deletion Mutations ◽  
Insertion And Deletion ◽  
Random Insertion

scholarly journals Effects of DNA heterologies on bacteriophage lambda recombination.

Genetics ◽  
1988 ◽  
Vol 118 (1) ◽  
pp. 13-19
Author(s):  
R K Pearson ◽  
M S Fox
Keyword(s):  
Bacteriophage Lambda ◽  
Indirect Evidence ◽  
Direct Products ◽  
Base Pairs ◽  
Heteroduplex Dna ◽  
Deletion Mutations ◽  
Genetic Crosses ◽  
Insertion And Deletion ◽  
Progeny Phage ◽  
Substitution Mutation

Abstract Previous studies of bacteriophage lambda recombination have provided indirect evidence that substantial sequence nonhomologies, such as insertions and deletions, may be included in regions of heteroduplex DNA. However, the direct products of heterology-containing heteroduplex DNA--heterozygous progeny phage--have not been observed. We have constructed a series of small insertion and deletion mutations in the cI gene to examine the possibility that small heterologies might be accommodated in heterozygous progeny phage. Genetic crosses were carried out between lambda cI- Oam29 and lambda cI+ Pam80 under replication-restricted conditions. Recombinant O+P+ progeny were selected on mutL hosts and tested for cI heterozygosity. Heterozygous recombinants were readily observed with crosses involving insertions of 4 to 19 base pairs (bp) in the cI gene. Thus, nonhomologies of at least 19 bp can be accommodated in regions of heteroduplex DNA during lambda recombination. In contrast, when a cI insertion or deletion mutation of 26 bp was present, few of the selected recombinants were heterozygous for cI. Results using a substitution mutation, involving a 26-bp deletion with a 22-bp insertion, suggest that the low recovery of cI heterozygotes containing heterologies of 26 bp or more is due to a failure to encapsulate DNA containing heterologies of 26 bp or more into viable phage particles.

Random Insertion and Deletion Mutagenesis

2003 ◽  
pp. 53-64 ◽  
Author(s):  
Hiroshi Murakami ◽  
Takahiro Hohsaka ◽  
Masahiko Sisido
Keyword(s):  
Deletion Mutagenesis ◽  
Insertion And Deletion ◽  
Random Insertion

scholarly journals Base insertion and deletion mutations induced in an Escherichia coli plasmid by benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide.

1981 ◽  
Vol 78 (11) ◽  
pp. 6817-6820 ◽  
Author(s):  
H. Mizusawa ◽  
C. H. Lee ◽  
T. Kakefuda ◽  
K. McKenney ◽  
H. Shimatake ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Deletion Mutations ◽  
Insertion And Deletion ◽  
Coli Plasmid ◽  
Base Insertion

scholarly journals Unique K-mer sequences for validating cancer-related substitution, insertion and deletion mutations

2020 ◽  
Author(s):  
HoJoon Lee ◽  
Ahmed Shuaibi ◽  
John M. Bell ◽  
Dmitri S. Pavlichin ◽  
Hanlee P. Ji
Keyword(s):  
Genome Sequencing ◽  
Somatic Mutations ◽  
Variant Calling ◽  
Cancer Genome ◽  
Sequencing Data ◽  
Deletion Mutations ◽  
Insertion And Deletion ◽  
Cancer Genome Sequencing ◽  
Significant Difference ◽  
Model Tuning

ABSTRACTThe cancer genome sequencing has led to important discoveries such as identifying cancer gene. However, challenges remain in the analysis of cancer genome sequencing. One significant issue is that mutations identified by multiple variant callers are frequently discordant even when using the same genome sequencing data. For insertion and deletion mutations, oftentimes there is no agreement among different callers. Identifying somatic mutations involves read mapping and variant calling, a complicated process that uses many parameters and model tuning. To validate the identification of true mutations, we developed a method using k-mer sequences. First, we characterized the landscape of unique versus non-unique k-mers in the human genome. Second, we developed a software package, KmerVC, to validate the given somatic mutations from sequencing data. Our program validates the occurrence of a mutation based on statistically significant difference in frequency of k-mers with and without a mutation from matched normal and tumor sequences. Third, we tested our method on both simulated and cancer genome sequencing data. Counting k-mer involving mutations effectively validated true positive mutations including insertions and deletions across different individual samples in a reproducible manner. Thus, we demonstrated a straightforward approach for rapidly validating mutations from cancer genome sequencing data.

Assessing the Effects of Amino Acid Insertion and Deletion Mutations

2021 ◽  
Author(s):  
Muneeba Jilani ◽  
Alistair Turcan ◽  
Nurit Haspel ◽  
Filip Jagodzinski
Keyword(s):  
Amino Acid ◽  
Deletion Mutations ◽  
Insertion And Deletion ◽  
Amino Acid Insertion
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