Single-sperm typing: determination of genetic distance between the G gamma-globin and parathyroid hormone loci by using the polymerase chain reaction and allele-specific oligomers.

Cui, Xiangfeng; Li, Honghua; Goradia, Tushar M.; Lange, Kenneth; Kazazian, Haig H.; Galas, David J.; Arnheim, Norman

doi:10.1073/pnas.86.23.9389

Cited by 178 publications

(126 citation statements)

References 13 publications

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“…24 Single sperm were sorted by flow cytometry into the wells of 96-well PCR plates and stored at À201C until use. Sperm lysis was performed prior to PCR according to Cui et al 50 …”

Section: Methodsmentioning

confidence: 99%

Determination of gene organization in the human IGHV region on single chromosomes

Pramanik

et al. 2005

Genes Immun

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Organization of the IGHV genes (n ¼ 108) on single human chromosomes has been determined by detecting these sequences in single sperm using multiplex PCR amplification followed by microarray detection. A total of 374 single sperm samples from five Caucasian males were studied. Three deletion/insertion polymorphisms (Del I-Del III) with deletion allele frequencies ranging from 0.1 to 0.3 were identified. Del I is a previously reported polymorphism affecting three IGHV genes (IGHV1-8, IGHV3-9, and IGHV2-10). Del II affects a region 2-18 kb containing two pseudogenes IGHV(II)-28.1 and IGHV3-29, and Del III spans B21-53 kb involving genes IGHV4-39, IGHV7-40, IGHV(II)-40-1, and IGHV3-41. Deletion alleles of both Dels II and III were found in a heterozygous state, and therefore, could not be easily detected if haploid samples were not used in the study. Results of the present study indicate that deletions/insertions together with other possible chromosomal rearrangements may play an important role in forming the genetic structure of the IGHV region, and may significantly contribute to antibody diversity. Since these three polymorphisms are located within or next to the 3 0 half of the IGHV region, they may have an important role in the expressed IGHV gene repertoire during immune response.

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“…24 Single sperm were sorted by flow cytometry into the wells of 96-well PCR plates and stored at À201C until use. Sperm lysis was performed prior to PCR according to Cui et al 50 …”

Section: Methodsmentioning

confidence: 99%

Determination of gene organization in the human IGHV region on single chromosomes

Pramanik

et al. 2005

Genes Immun

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“…Second, unlike yeast, where cells can be induced to synchronously enter sporulation and initiate meiosis (Govin and Berger 2009), meiotic progression is asynchronous in mammals and at any given moment <2% of the cells in the mouse gonads contain DSBs (Bellve et al 1977;Meistrich 1977). Unfortunately, sperm genotyping (Li et al 1988;Cui et al 1989;Hogstrand and Bohme 1994)-the method of choice for high-resolution recombination hotspot mapping in mammals-does not scale to genome-wide applications (for reviews, see Arnheim et al 2007;Kauppi et al 2009;Paigen and Petkov 2010).…”

mentioning

confidence: 99%

Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA

Khil¹,

Smagulova²,

Brick³

et al. 2012

Genome Res.

121

139

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Meiotic DNA double-stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. DSBs can be directly mapped using chromatin immunoprecipitation followed by sequencing (ChIPseq). Nevertheless, the genome-wide mapping of recombination hotspots in mammals is still a challenge due to the low frequency of recombination, high heterogeneity of the germ cell population, and the relatively low efficiency of ChIP. To overcome these limitations we have developed a novel method-single-stranded DNA (ssDNA) sequencing (SSDS)-that specifically detects protein-bound single-stranded DNA at DSB ends. SSDS comprises a computational framework for the specific detection of ssDNA-derived reads in a sequencing library and a new library preparation procedure for the enrichment of fragments originating from ssDNA. The use of our technique reduces the nonspecific double-stranded DNA (dsDNA) background >10-fold. Our method can be extended to other systems where the identification of ssDNA or DSBs is desired.

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“…The estimated probability that siblings will have identical genotypes for these 40 SNPs is 0.5 raised to the power of the number of SNPs used (40) since all of these markers have alleles close to 50:50 in the population. Therefore, the likelihood of observing identity of two full siblings is approximately 1 in 1 X 10 12 . An experimental estimate of likelihood of siblings with full identity was obtained using publically available and newly obtained data from 405 samples.…”

Section: Experimental Designmentioning

confidence: 99%

“…Two-cell (n=12) or 5-cell (n=12) samples to model the number of cells obtained from trophectoderm biopsy) were removed from 3 of the sibling cell lines (GM11870, GM11872, GM11873) using a 100 μm stripper tip and pipet (MidAtlantic Diagnostics), under a dissecting microscope, and placed into a nuclease-free 0.2 ml PCR tube (Ambion Inc., Austin, TX) in a volume of 1 μl media for subsequent qPCR. Cell line samples were processed by alkaline lysis as previously described [12]. All cell line DNA samples were blinded before qPCR analysis as described below.…”

Section: Sibling Identity Likelihoodmentioning

confidence: 99%

Trophectoderm DNA fingerprinting by quantitative real-time PCR successfully distinguishes sibling human embryos

Scott

Tao

et al. 2014

J Assist Reprod Genet

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Purpose To validate a novel and more practical system for trophectoderm DNA fingerprinting which reliably distinguishes sibling embryos from each other. Methods In this prospective and blinded study two-cell and 5-cell samples from commercially available sibling cell lines and excess DNA from trophectoderm biopsies of sibling human blastocysts were evaluated for accurate assignment of relationship using qPCR-based allelic discrimination from 40 single nucleotide polymorphisms (SNPs) with low allele frequency variation and high heterozygosity. Results Cell samples with self relationships averaged 95.1± 5.9 % similarity. Sibling relationships averaged 57.2±5.9 % similarity for all 40 SNPs, and 40.8±8.2 % similarity for the 25 informative SNPs. Assignment of relationships was accomplished with 100 % accuracy for cell lines and embryos. Conclusions These data demonstrate the first trophectoderm qPCR-based DNA fingerprinting technology capable of unequivocal discrimination of sibling human embryos. This methodology will empower research and development of new markers of, and interventions that influence embryonic reproductive potential.

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Single-sperm typing: determination of genetic distance between the G gamma-globin and parathyroid hormone loci by using the polymerase chain reaction and allele-specific oligomers.

Cited by 178 publications

References 13 publications

Determination of gene organization in the human IGHV region on single chromosomes

Determination of gene organization in the human IGHV region on single chromosomes

Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA

Trophectoderm DNA fingerprinting by quantitative real-time PCR successfully distinguishes sibling human embryos

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