Plasma-derived cell-free mitochondrial DNA: A novel non-invasive methodology to identify mitochondrial DNA haplogroups in humans.

BACKGROUND: Mitochondrial diseases are a clinically heterogeneous group of diseases caused by mutations in either nuclear or mitochondrial DNA (mtDNA). The diagnosis is challenging and has frequently required a tissue biopsy to obtain a sufficient quantity of mtDNA. Less-invasive sources mtDNA, such as peripheral blood leukocytes, urine sediment, or buccal swab, contain a lower quantity of mtDNA compared to tissue sources which may reduce sensitivity. Cellular apoptosis of tissues and hematopoetic cells releases fragments of DNA and mtDNA into the circulation and these molecules can be extracted from plasma as cell-free DNA (cfDNA). However, entire mtDNA has not been successfully identified from the cell free fraction previously. We hypothesized that the circular nature of mtDNA would prevent its degradation and a higher sensitivity method, such as next generation sequencing, could identify intact cf-mtDNA from human plasma. METHODS: Plasma was obtained from patients with mitochondrial disease diagnosed from skeletal muscle biopsy (n = 7) and healthy controls (n = 7) using a specially cfDNA collection tube (Streck Inc.; La Vista, NE). To demonstrate the presence of mtDNA within these samples, we amplified the isolated DNA using custom PCR primers specific to overlapping fragments of mtDNA. cfDNA samples were then sequenced using the Illumina MiSeq sequencing platform. RESULTS: We confirmed the presence of mtDNA, demonstrating that the full mitochondrial genome is in fact present within the cell-free plasma fraction of human blood. Sequencing identified the mitochondrial haplogroup matching with the tissue specimen for all patients. CONCLUSION: We report the existence of full length mtDNA in cell-free human plasma that was successfully used to perform haplogroup matching. Clinical applications for this work include patient monitoring for heteroplasmy status after mitochondrially-targeted therapies or haplogroup monitoring as a measure of stem cell transplantation.

High-resolution mapping of the Drosophila fourth chromosome using site-directed terminal deficiencies.

For more than 80 years, the euchromatic right arm of the Drosophila fourth chromosome (101F-102F) has been one of the least genetically accessible regions of the fly genome despite the fact that many important genes reside there. To improve the mapping of genes on the fourth chromosome, we describe a strategy to generate targeted deficiencies and we describe 13 deficiencies that subdivide the 300 kb between the cytological coordinates 102A6 and 102C1 into five discrete regions plus a 200-kb region from 102C1 to 102D6. Together these deficiencies substantially improve the mapping capabilities for mutant loci on the fourth chromosome.

Toward optimal detection of the common prenatal aneuploidies by quantitative fluorescent-polymerase chain reaction: comparison of two commercial assays.

BACKGROUND/AIM: To evaluate and compare the performance of the recently released Aneufast™ v2 (MolgentixSL) and QST*RplusV2 commercial assays (Gen-Probe), both designed for the quantitative fluorescent-polymerase chain reaction (PCR) detection of the common aneuploidies during pregnancy. METHODS: A series of 160 consecutive fetal samples referred for rapid aneuploidy detection testing and an additional 25 samples enriched for the presence of an abnormality were selected for comparison. RESULTS: To confidently rule out a chromosome abnormality, a second round of short tandem repeat typing was required for 14.1% (26) and 9.7% (18) of the specimens analyzed with Aneufast v2 and QST*RplusV2, respectively. Reflex testing was required for 7.6% (14) and 5.9% (11) of the specimens analyzed with respective assays to confidently rule out an autosomal trisomy. For the sex chromosomes, the difference in the amount of follow-up testing is greater between the assays, as a result of the inclusion in the initial PCR of the TAF9L paralogous marker in the QST*RplusV2 assay. CONCLUSIONS: Overall, both assays performed similarly in the detection of aneuploidies. In this sample set, the QST*RplusV2 kit required less frequent reflex testing, which translates into shorter turnaround time and cost savings. The incorporation of the TAF9L paralogous sequence in the initial PCR is advantageous for diagnostic use.

Drosophila Activin- and the Activin-like product Dawdle function redundantly to regulate proliferation in the larval brain.

The Drosophila Activin-like ligands Activin-beta and Dawdle control several aspects of neuronal morphogenesis, including mushroom body remodeling, dorsal neuron morphogenesis and motoneuron axon guidance. Here we show that the same two ligands act redundantly through the Activin receptor Babo and its transcriptional mediator Smad2 (Smox), to regulate neuroblast numbers and proliferation rates in the developing larval brain. Blocking this pathway results in the development of larvae with small brains and aberrant photoreceptor axon targeting, and restoring babo function in neuroblasts rescued these mutant phenotypes. These results suggest that the Activin signaling pathway is required for producing the proper number of neurons to enable normal connection of incoming photoreceptor axons to their targets. Furthermore, as the Activin pathway plays a key role in regulating propagation of mouse and human embryonic stem cells, our observation that it also regulates neuroblast numbers and proliferation in Drosophila suggests that involvement of Activins in controlling stem cell propagation may be a common regulatory feature of this family of TGF-beta-type ligands.

Molecular mapping of deletion breakpoints on chromosome 4 of Drosophila melanogaster.

As part of our effort to induce and identify mutations in all genes on chromosome 4 of Drosophila melanogaster, we have mapped the breakpoints of eight chromosome 4 deficiencies relative to the predicted genes along this chromosome. Although the approximate locations of Df(4)G, Df(4)C3, Df(4)M101-62f, Df(4)M101-63a, Df(4)J2, Df(4)O2, Df(4)C1-10AT, and Df(4)B2-2D are known (some from cytological observations and others predicted from P element locations), the extents of these deletions have not been mapped with respect to the predicted genes identified by the Drosophila Genome Project. Polymerase chain reaction primers were designed to amplify the predicted exons of all chromosome 4 genes, and homozygous embryos for each deficiency were identified and their DNA used to test for the presence or absence of these exons. By testing for the inability to amplify various exons along the length of the chromosome, we were able to determine which predicted genes are missing in each deficiency. The five deficiencies, Df(4)G, Df(4)C3, Df(4)C1-10AT, and Df(4)B2-20 (all terminal deletions), and Df(4)M101-62f (a proximal interstitial deletion), enabled us to partition the gene-containing, right arm of chromosome 4 into five regions. Region A [uncovered by Df(4)M101-62f] contains the proximal-most 21 genes; region B [uncovered by Df(4)B2-2D] contains the next 12 genes; region C [uncovered by Df(4)B2-2D and Df(4)C1-10AT] contains the next 17 genes; region D [uncovered by Df(4)B2-2D, Df(4)C1-10AT, and Df(4)C3] contains the next 21 genes; and region E [uncovered by Df(4)B2-2D, Df(4)C1-10AT, Df(4)C3, and Df(4)G] contains the distal-most ten genes. By using Df(4)M101-62f, Df(4)B2-2D, Df(4)C1-10AT, Df(4)C3, and Df(4)G in complementation tests, we can assign newly induced recessive lethal mutations to one of the five regions on chromosome 4. This will substantially reduce the amount of DHPLC analysis required to match each mutation to a predicted transcript on chromosome 4.