Identification of Balanced Chromosomal Rearrangements Previously Unknown Among Participants in the 1000 Genomes Project: Implications for Interpretation of Structural Variation in Genomes and the Future of Clinical Cytogenetics

Purpose Recent studies demonstrate that whole-genome sequencing (WGS) enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in The 1000 Genomes Project without knowing affected bands. Methods: The 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparently BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories. We applied our analytical tool to 1,166 genomes from the 1000 Genomes Project with sufficient physical coverage (8.25-fold). Results: Our approach detected four reciprocal balanced translocations and four inversions ranging in size from 57.9 kb to 13.3 Mb, all of which were confirmed by cytogenetic methods and PCR studies. One of DNAs has a subtle translocation that is not readily identified by chromosome analysis due to similar banding patterns and size of exchanged segments, and another results in disruption of all transcripts of an OMIM gene. Conclusions: Our study demonstrates the extension of utilizing low-coverage WGS for unbiased detection of BCAs including translocations and inversions previously unknown in the 1000 Genomes Project

Biochemical studies and heterologous expression of 1-Aminocyclopropane-1-Carboxylic Acid N-Malonyltransferase from munghbean hypocotyls

abstracttocpublished_or_final_versionZoologyMasterMaster of Philosoph

Generation of escape SARS-CoV mutant virus in the presence of mAb 1A9.

<p>Human SARS-CoV HKU39849 strain was cultured in Vero E6 cells in the absence or presence of mAb 1A9 (0.25 mg/ml). Supernatant from the wells containing cells that exhibited cytopathic effect (CPE) at the highest dilution of SARS-CoV was harvested as passage 1. The virus was then passaged 3 times in the presence of mAb 1A9 (0.25 mg/ml) and the virus supernatant harvested at each passage was titrated on Vero E6 cells.</p

Determination of cell surface expression of wild-type and mutant D1128A S proteins by FACS analysis and determination of wild-type and mutant D1128A S protein incorporation in S-pp by ELISA.

<p>(A) FACS analysis was performed with 293 FT cells were transfected with empty vector (full line) or with plasmids expressing full length wild-type S (dotted line) or full length mutant D1128A S (dash line). Cells were harvested 72 hours post-transfection and stained with mouse mAb 7G12, followed by FITC-conjugated goat anti-mouse antibody. Results shown are representative of 3 independent experiments. (B) Pseudoviral particles not expressing S (pNL43-R-E-Luc virus), S-pp expressing wild-type S (S-WT-pp) and mutant D1128A S (S-D1128A-pp) were coated on a 96-well plate at 16 ng/well, as previously quantitated using P24 ELISA, and detected using mAb 7G12 (top) and mAb P24 (bottom) at 4-fold serial dilutions. Optical density (OD) was measured at 450 nm. Bars represent SD of the experiment carried out in triplicates. MAb P24 was used as a control antibody to ensure equal amounts of S-pp were coated onto each well.</p

Neutralization of wild-type, mutant D1128A, N1056K and D1128A/N1056K S-pps by mAb 1A9 and mAb 1G10.

<p>S-pp containing wild-type (S-WT-pp) or mutant S (S-D1128A-pp, S-N1056K-pp and S-D1128A/N1056K-pp) were pre-incubated with different concentrations of (A) mAb 1A9 or (B) mAb 1G10 at 25, 50, 100 and 200 µg/ml for 1 hour before infecting CHO-ACE2 cells. An anti-S1, non-neutralizing mAb 7G12 was used as control antibody at 200 µg/ml. Cells were harvested 48 hours post-infection and luciferase activities were measured. Viral entry, as indicated by the luciferase activity measured in relative light units (RLU), was expressed as a percentage of the reading obtained in the absence of antibody, which was set at 100%. Data shown represents that obtained from 3 independent experiments. Bars represent SD of the experiment carried out in triplicates. *indicates statistically significant difference of <i>p</i><0. 01 when compared to S-WT-pp.</p

Neutralization of wild-type and 1A9 escape SARS-CoV virus by mAb 1A9 and mAb 1G10.

<p>Wild-type human SARS-CoV HKU39849 strain (A and C) and escape mutant SARS-CoV virus generated in the presence mAb 1A9 (B and D) were used at 1000 TCID₅₀ to infect Vero E6 cells in the presence of two mAbs, namely mAb 1A9 (A and B) and mAb 1G10 (C and D). MAb 1A9 was used at concentrations 0, 0.25, 0.5, 1.0 and 2.0 mg/ml while mAb 1G10 was used at concentrations 0, 0.125, 0.25, 0.5 and 1.0 mg/ml. Percentage cytopathic effects (% CPE) of the infected cells was observed. MAb 1G10, a SARS-CoV-neutralizing, anti-S2 mAb that binds to S2 at residues 1151–1192, was used as the control mAb.</p

Binding of mAb 1A9 to wild-type, mutant D1128A, mutant N1056K and mutant D1128A/N1056K S proteins by Western Blot and immunoprecipitation.

<p>293(mock) or with plasmids expressing full length wild-type S (S-WT) or full length mutant S (S-D1128A, S-N1056K and S-D1128A/N1056K). (A) Western Blot analysis was performed on the cell lysates using mAb 1A9 to determine if it can bind to the different S proteins. MAb 7G12, which binds to the S1 of the S protein, was used as a control antibody to detect protein expression. (B) Cell lysates containing S-WT, S-D1128A, S-N1056K or S-D1128A/N1056K were subjected to immunoprecipitation (IP) using mAb 1A9 or 7G12 and protein A beads. S proteins immunoprecipitated by mAbs 1A9 and 7G12 were detected using rabbit anti-SΔ1 antibody in Western blot analysis (WB). The rabbit anti-SΔ1 antibody binds to amino acids 48–358 of the S1 subunit.</p

Binding and neutralization of human, civet SARS-CoVs and bat SL-CoVs to mAb 1A9.

<p>(A) Schematic representation of chimeric S protein of civet SARS-CoV SZ3, bat SL-CoVs Rp3 and Rf1. The civet SARS-CoV SZ3 chimeric S contains four mutations (R344K, S360F, K479N and S485T) at its RBD that is different from the RBD of human SARS-CoV HKU39849. The bat SL-CoVs Rp3 and Rf1 chimeric S proteins had their entire RBD (amino acids 322–496) replaced by the RBD of human SARS-CoV HKU39849 (amino acids 318–518). (B) 293 FT cells were transfected with no plasmid (mock) or with plasmids expressing S of human SARS-CoV HKU39849, RBD-modified chimeric S of civet SARS-CoV SZ3, bat SL-CoV Rp3 and Rf1 respectively. Western Blot analysis was performed on the cell lysates using mAb 1A9 to determine if it can bind to different S proteins. MAb 7G12, which binds to the S1 of the S protein, was used as a control antibody to detect protein expression. (C) S-pps containing S of human HKU39849, civet SZ3, bat Rp3 or Rf1, were pre-incubated with different concentrations of mAb 1A9 at 100, 150 and 200 µg/ml for 1 hour before infecting CHO-ACE2 cells. Cells were harvested 48 hours post-infection and luciferase activities were measured. Viral entry, as indicated by the luciferase activity measured in relative light units (RLU), was expressed as a percentage of the reading obtained in the absence of antibody, which was set at 100%. Data shown represents that obtained from 3 independent experiments. Bars represent SD of the experiment carried out in triplicates.</p