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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
.../or neuromuscular outcomes. They occur when a segment of repetitive DNA, termed a short tandem repeat (STR), expands beyond a gene-specific threshold. STR is composed of tandem arrays of 1–12 bp sequence motifs and constitute ∼6% of the human (Willems et al. 2014; Mousavi et al. 2019). To date, the genetic basis...
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METHODS: High-Precision Genotyping by Denaturing Capillary Electrophoresis
- H.-Michael Wenz,
- James M. Robertson,
- Steve Menchen,
- Frank Oaks,
- David M. Demorest,
- Don Scheibler,
- Barnett B. Rosenblum,
- Carla Wike,
- Dennis A. Gilbert,
- and J. William Efcavitch
Genome Res. January 1, 1998 8: 69-80; doi:10.1101/gr.8.1.69
...Techniques 14 : 98 – 111 . ↵ Mansfield E.S. , Vainer M. , Enad S. , Barker D.L. , Harris D. , Rappaport E. , Fortina P. ( 1996 ) Sensitivity, reproducibility, and accuracy in short tandem repeat genotyping using capillary array electrophoresis. Genome Res. 6 : 893 – 903 . ↵ Mikkers F.E.P. , Everaerts F...
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METHODS: Loss of Heterozygosity Assay for Molecular Detection of Cancer Using Energy-transfer Primers and Capillary Array Electrophoresis
- Igor L. Medintz,
- Chyi-Chia Richard Lee,
- Wendy W. Wong,
- Kristin Pirkola,
- David Sidransky,
- and Richard A. Mathies
Genome Res. August 1, 2000 10: 1211-1218; doi:10.1101/gr.10.8.1211
.... , Barker D. , Johnston R. ( 1996b ) Implementation of a capillary array electrophoresis instrument. J. Cap. Electrophor. 3 : 61 – 68 . ↵ Edwards A. , Civitello A. , Hammond H.A. , Caskey C.T. ( 1991 ) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Amer. J. Hum. Genet. 49 : 746...
REVIEW: An approach to high-throughput genotyping.
- J M Hall,
- C A LeDuc,
- A R Watson,
- and A H Roter
Genome Res. September 1996 6: 781-790; doi:10.1101/gr.6.9.781
..., G. , Mathies. R. Wang, Y., Ju, J. Carpenter, B. Atherton, J. Sensabaugh, G. and Mathies. R. 1995 . Rapid sizing of short tandem repeat alleles using capillary array electrophoresis and energy-transfer fluorescent primers. Anal. Chem. 67 : 1197 – 1203 . Weeks, D.E. , Lathrop. G.M. Weeks, D...
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LETTER: Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
- Wei Zhang,
- Weihong Qi,
- Thomas J. Albert,
- Alifiya S. Motiwala,
- David Alland,
- Eija K. Hyytia-Trees,
- Efrain M. Ribot,
- Patricia I. Fields,
- Thomas S. Whittam,
- and Bala Swaminathan
Genome Res. June 2006 16: 757-767; Published in Advance April 10, 2006, doi:10.1101/gr.4759706
...on the informative synonymous SNPs was compared to the maximum parsimony trees inferred from pulsed-field gel electrophoresis and multilocus variable numbers of tandem repeats analysis. The topological discrepancies indicate that, in contrast to the synonymous mutations, parts of STEC O157 genomes have evolved...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...to measure extreme length values (e.g., >250 CGG for FMR1 repeats) (Chen et al. 2011). While genotyping software has facilitated the simultaneous detection of multiple tandem repeats using short reads, the repeat lengths require sufficient coverage at the locus and are estimated rather than precisely...
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ARTICLE: Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27
- Natalay Kouprina,
- Adam Pavlicek,
- Vladimir N. Noskov,
- Greg Solomon,
- John Otstot,
- William Isaacs,
- John D. Carpten,
- Jeffrey M. Trent,
- Joanna Schleutker,
- J. Carl Barrett,
- Jerzy Jurka,
- and Vladimir Larionov
Genome Res. November 2005 15: 1477-1486; doi:10.1101/gr.4212705
..., two, or three copies of the SPANX-B gene. ( B ) Genomic DNA from 28 individuals (11 cases and 18 controls) was digested with BamHI, CHEF gel electrophoresis-separated, and blot-hybridized with a specific probe to reveal the presence of a 12-kb SPANX-B tandem repeat. The figure shows only 13...

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