The biochemical and genetic diagnosis of lipid disorders.

PURPOSE OF REVIEW: To examine recent advances in our knowledge on the diagnosis of lipid disorders. RECENT FINDINGS: Fasting values above the 99th percentile for direct LDL-cholesterol (LDL-C), lipoprotein(a), and triglycerides are greater than 225 mg/dl, greater than 160 mg/dl, and greater than 500 mg/dl (>5.82, >394, and >5.65 mmol/l), respectively, whereas such values for plasma lathosterol, ß-sitosterol, and cholestanol are greater than 8.0, 8.0, and 5.0 mg/l (>0.021, 0.019, and 0.013 mmol/l), respectively. Values below the first percentile for LDL-C are less than 40 mg/dl (<1.03 mmol/l) and for HDL-cholesterol (HDL-C) less than 25 mg/dl (<0.65 mmol/l) in men and less than 30 mg/dl (<0.78 mmol/l) in women, respectively. The above values can predispose to premature CVD, pancreatitis, neurologic disease, and kidney failure, and may be associated with monogenic lipid disorders. In the absence of secondary causes including diabetes or kidney, liver, or thyroid disease, consideration should be given to sequencing the following genes: ABCA1, ABCG5, ABCG8, APOA1, APOA5, APOB, APOC2, APOE, CETP, CYP27A1, GPIHBP1, LCAT, LDLR, LDLRAP1, LIPA, LIPC, LMF1, LPL, MTTP, PCSK9, SCARB1, and STAP1. SUMMARY: Recent data indicate that secondary causes and a wider range of conditions need to be considered in identifying the underlying causes of hypercholesterolemia, hypertriglyceridemia, hyperalphalipoproteinemia, hypobetalipoproteinemia, and HDL deficiency. Identifying such disorders allows for a more precise assessment of prognosis and the formulation of optimal therapy.

Cervical adenocarcinoma identification by testing for chromosomal abnormalities.

We report on a case of cervical adenocarcinoma in situ in a 42-year-old woman with a history of human papillomavirus infection. Repeat cytology, human papillomavirus testing, and colposcopy failed to identify the lesion. Testing of the cervical cell DNA identified chromosomal abnormalities, prompting a cervical cone biopsy, which identified adenocarcinoma in situ.

Bridging expressed sequence alignments through targeted cDNA sequencing.

One of the major challenges in genome research is the identification of the complete set of genes in a genome. Alignments of expressed sequences (RNA and EST) with genomic sequences have been used to characterize genes. However, the number of alignments far exceeds the likely number of genes in a genome, suggesting that, for many genes, two or more alignments can be joined through overlapping sequences to yield accurate gene structures. High-throughput EST sequencing becomes less efficient in closing those alignment gaps due to its nonselective nature. We sought to bridge these alignments through a novel approach: targeted cDNA sequencing. Human expressed sequences from GenBank version 124 were aligned with the genomic sequence from NCBI build 24 using LEADS, Compugen's EST and RNA clustering and assembly software system. Nine hundred forty-eight pairs of alignments were selected based on EST clone information and/or their homology to the same known proteins. Reverse transcriptase PCR and sequencing yielded sequences for 363 of those pairs. These sequences helped characterize over 60 novel or otherwise incomplete genes in the recent UniGene build 153, which included over 1 million additional ESTs. These results indicate that this integrated and targeted strategy, combining computational prediction and experimental cDNA sequencing, can efficiently generate the overlapping sequences and enable the full characterization of genomes. Additional information about the contig pairs, the resultant overlapping sequences, tissue sources, and tissue profiles are available in a supplemental file.

C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.

To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1), of which roughly 4,000 correspond to genes that are untouched by any cDNA or expressed-sequence tag (EST). More than 50% of predicted genes needed corrections in their intron-exon structures. Notably, approximately 11,000 C. elegans proteins can now be expressed under many conditions and characterized using various high-throughput strategies, including large-scale interactome mapping. We suggest that similar ORFeome projects will be valuable for other organisms, including humans.