Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases.

BACKGROUND: Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS: In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS: Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS: Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.

Vertical stratification of the air microbiome in the lower troposphere.

The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface.

Breast MRI findings after modified radical mastectomy and transverse rectus abdominis myocutaneous flap in patients with breast cancer.

PURPOSE: To evaluate the MRI findings in breast cancer patients who had undergone a modified radical mastectomy (MRM) and a transverse rectus abdominis myocutaneous (TRAM) flap. MATERIALS AND METHODS: MRI was performed on 20 patients who had been diagnosed with breast cancer and had undergone an MRM and TRAM flap. The results were examined in terms of MRI's ability to detect the flap and assess possible postoperative changes and recurrence. In addition, MRI images of the opposite breast were analyzed. Follow-up examinations were carried out on 11 patients, and all changes were assessed. RESULTS: The flap was clearly visualized by MRI in all of the patients. The signal intensity of the flap was equivalent to that of fat. The contact zone between the TRAM flap and the mastectomy site was enhanced after contrast infusion. Postoperative changes, such as skin thickening (n=20), edema (n=2), fluid collection (n=3), hematoma (n=1), and fat necrosis (n=3), were detected. In two patients, artificially inserted fat tissue was identified. On the MRI of the opposite breast, enhancing lesions were detected in seven patients. In one patient with this finding, ductal carcinoma in situ was diagnosed. On the follow-up MRI, a decrease in skin thickening, fat necrosis, and hematoma was detected. CONCLUSION: MRI is an effective method for lesion detection and evaluation of postoperative changes after MRM and TRAM flap, as well as for evaluation of the opposite breast.

Sonographic findings in a patient with cystic hypersecretory duct carcinoma of the breast.

In this report, we describe a case of a rare form of intraductal carcinoma of the breast known as cystic hypersecretory duct carcinoma in a 49-year-old woman with a palpable mass and no history of breast disease. Mammography showed heterogeneous dense breast tissue with no definite abnormally increased density or microcalcifications. Gray-scale sonography detected multiple small aggregated, anechoic cysts with good through-transmission in the upper outer quadrant of the left breast, corresponding to the location of the palpable mass. The patient underwent an excision biopsy, and histopathologic examination of the surgical specimen revealed multiple cysts of different size containing an eosinophilic material resembling thyroid colloid. The locations of the cysts corresponded to those of the anechoic cysts detected on sonography. The epithelium lining the cysts showed micropapillary growth consistent with a diagnosis of cystic hypersecretory duct carcinoma. The mammographic and sonographic findings in this case differed somewhat from those reported previously for this rare form of breast carcinoma. Because the imaging findings and low-power microscopic appearance of the mass in our patient's case closely resembled those of some benign breast lesions, we recommend careful differentiation of this type of lesion using high-power microscopy during histopathologic evaluation.