Understanding falls and its prevention among adults with visual impairment through behavior change models

SIGNIFICANCE

This study used behavior change models to understand the perspectives of falls among patients with visual impairment who are at greater risk of falls. Resulting themes on barriers and facilitators led to the identification of a "SMART" intervention strategy that remains to be tested as a fall-reducing behavior.

PURPOSE

This study explored the perspectives of adults with visual impairment on falls and proposed falls prevention strategies using behavior change models.

METHODS

Participants 18 years or older who were diagnosed with low vision or blindness from a tertiary eye hospital in India and had a history of falls in the previous year were recruited. "Reduction of falls" was defined as a behavior, and interview questions were designed to explore awareness, context, and consequences of falls to determine barriers and facilitators that could help reduce falls. The interviews were audio-recorded, transcribed, translated into English, and analyzed using thematic analysis. The results were linked to the Theoretical Domains Framework and the Behavior Change Wheel, under different levels of a The Socio-Ecological Model. Intervention functions from the Behavior Change Wheel were identified using the APEASE criteria (affordability, practicability, effectiveness/cost-effectiveness, acceptability, safety/side effects, and equity) to finalize behavior change techniques.

RESULTS

Themes on barriers and facilitators at individual, family, and societal levels were identified from 36 semistructured telephone interviews. Key barriers were fear of falling, social stigma and lack of training in using assistive devices, not considering falls as a major concern, environmental hazards, and loss of support from caregivers. Key facilitators were consciously monitoring falls, undergoing orientation and mobility training, getting assistance for outdoor mobility, and self-confidence.

CONCLUSIONS

This study proposed a five-step "SMART" intervention strategy for prevention of falls to be prospectively tested. SMART include Support from caregivers and use of assistive devices, Monitoring of falls, Awareness about falls, Reduction of hazards, and Training for safe mobility.

Choriocapillaris flow deficits in polypoidal choroidal vasculopathy using swept source optical coherence tomography angiography

Purpose:

To evaluate the choriocapillaris flow deficits (CCFD) on swept-source optical coherence tomography angiography (SS-OCTA) in eyes with unilateral polypoidal choroidal vasculopathy (PCV), fellow unaffected eyes, and to compare them with age-matched healthy controls.

Methods:

This study was a cross-sectional study which included treatment-naïve eyes with unilateral PCV (group 1), fellow unaffected eyes of patients with PCV (group 2), and normal eyes (group 3). Using the SS-OCTA, the Choriocapillaris (CC) slab was segmented from the structural optical coherence tomography (OCT) and the corresponding flow map was multiplied after signal compensation. The resultant image was evaluated for CCFD in equidistant squares measuring 1 × 1 mm, 1.5 × 1.5 mm, 2 × 2 mm, 2.5 × 2.5 mm, 3 × 3 mm, and 6 × 6 mm centered on the fovea.

Results:

The percentage of flow deficits were significantly increased (one-way ANOVA, P = 0.003 and P = 0.049) in the eyes with PCV as compared to the fellow eyes, and age-matched healthy controls. In the multiple pairwise comparison using post hoc Bonferroni, CCFD of 1 mm in group 1 and 2 (P = 0.019), group 1 and 3 (P = 0.003), and CCFD of 1.5 mm in group 1 and 3 (P = 0.044) were statistically significant. Correlation analysis showed no significant correlation between CCFD, age, Best corrected visual acuity (BCVA), foveal thickness (FT), and subfoveal choroidal thickness (SFCT) in our study. Linear regression analysis showed that the CCFD was negatively correlated with the distance from the foveal center in group 1 (β = −0.613, P = 0.046).

Conclusion:

Eyes with PCV demonstrated a significant flow impairment in the choriocapillaris layer as compared to the fellow unaffected eyes and age-matched healthy eyes.

Structural and functional changes among diabetics with no diabetic retinopathy and mild non-proliferative diabetic retinopathy using swept-source optical coherence tomography angiography and photopic negative response

PURPOSE

To assess the structural and functional changes among diabetics with no diabetic retinopathy (NDR) and mild non-proliferative diabetic retinopathy (NPDR) using swept-source optical coherence tomography angiography (SSOCTA) and photopic negative response (PhNR) and to find the earliest changes.

METHODS

This was a prospective, cross-sectional, case-control study. Participants with minimum 5 years of diabetes mellitus (DM) were recruited and classified as NDR and mild NPDR based on fundus findings. Age-matched normals with nil ocular pathology were considered as controls. SSOCTA scan acquisition (6*6 mm angiography), followed by full field photopic electroretinography (FFERG) and red on blue PhNR (R/B PhNR) were done with complete pupillary dilatation.

RESULTS

A total of 88 participants were included with 35 controls, 39 NDR and 14 mild NPDR subjects. Vessel density of the superficial capillary plexus (SCP) and deep capillary plexus (DCP) of mild NPDR were significantly reduced compared to the controls (17.12 ± 2.65 mm^-1 vs. 18.75 ± 0.90 mm^-1, p = 0.025 and 7.96 ± 3.92 mm^-1 vs. 11.83 ± 3.05 mm^-1, p = 0.001 respectively). None of the parameters of controls had significant difference compared to NDR group (p > 0.05). The amplitudes of white on white (W/W) a-wave, W/W b-wave, red on blue (R/B) PhNR baseline to trough (BT) and R/B PhNR peak to trough in controls were significantly high compared to NDR and mild NPDR. Amplitude of R/B PhNR BT had the maximum area under the curve of 75.9% with a sensitivity and specificity of 94.3and 77.4%, respectively.

CONCLUSION

A significant decrease in functional changes as measured by ERG especially PhNR, is seen even among the NDR group compared to controls unlike SSOCTA parameters that measures very early vascular structural changes. PhNR is a sensitive test to identify early preclinical changes in DR when microvascular structural changes as determined by SSOCTA are normal.

Retino-choroidal evaluation of the macular region in eyes with tubercular serpiginous-like choroiditis using swept-source optical coherence tomography angiography

AIM

To analyse the alterations in retino-choroidal angioarchitecture in eyes with active tubercular serpiginous-like choroiditis (TB-SLC) using swept-source optical coherence tomography angiography (SS-OCTA).

METHODS

This prospective cross-sectional study enrolled 34 eyes diagnosed with TB-SLC and 34 age-matched healthy controls. Data acquisition with SS-OCTA using the PLEX Elite 9000 (Carl Zeiss Meditec Inc., Dublin, CA, USA) with a 6 × 6 mm pattern centered on the foveal center was done. Automated retinal vessel length density (VLD) and perfusion density (PD) and foveal avascular zone architecture were obtained from the ARI hub. Choroidal vascularity index (CVI) and choriocapillaris flow deficits (CCFD) were obtained using Image J.

RESULTS

Eyes with TB-SLC showed significantly reduced vessel indices in all retinal layers (P < 0.05), decreased CVI (P = 0.001) and increased CCFD (P = 0.001) as compared to healthy eyes. CCFD was increased significantly in the involved quadrants in eyes with TB-SLC when compared with the uninvolved quadrants and corresponding healthy quadrants in control subjects. CCFD showed a significant negative correlation with visual acuity (r = - 0.46, P = 0.006).

CONCLUSION

Eyes with TB-SLC manifest reduced VLD and PD, decreased CVI and increased CCFD. The CCFD alterations are non-uniform in these eyes, mainly located under the regions with disease activity.

Comparison of broadband and monochromatic photopic negative response in eyes of patients with diabetes with no diabetic retinopathy and different stages of diabetic retinopathy

Purpose:

To evaluate the change in broadband (W/W), red on blue (R/B), and blue on yellow (B/Y) photopic negative response (PhNR) in patients with diabetes mellitus with no diabetic retinopathy (no DR) and different stages of DR and compare it with age-matched controls. This study was performed to provide a single PhNR protocol that can be used for early diagnosis of DR.

Methods:

It was a cross-sectional case-control study done in a hospital setup. Patients with diabetes with no DR and different stages of DR with no other associated ocular pathologies were included. Age-matched controls with no retinal pathologies were also included for comparison. All subjects underwent detailed ophthalmic examination and W/W, R/B, and B/Y electroretinography. Fifty control eyes and 52 treatment naïve eyes of 52 patients with diabetes [no DR = 11, mild nonproliferative diabetic retinopathy (NPDR) =11, moderate NPDR = 10, severe NPDR = 9, and proliferative DR = 11] were included in the study.

Results:

On comparing the ERG responses in patients with diabetes and age-matched controls, a significant reduction (P < 0.05) was noted in the amplitudes of a-wave (39.78 ± 11.34 μV vs. 67.28 ± 12.88 μV), b-wave (116.25 ± 45.25 vs. 134.39 ± 28.78 μV), W/W PhNR (33.86 ± 17.33 vs. 67.18 ± 15.99 μV), R/B PhNR (28.77 ± 15.85 vs. 53.48 ± 14.15 μV), and B/Y PhNR (55.04 ± 32.63 vs. 104.79 ± 24.37 μV). Posthoc analysis revealed that all the eyes in the diabetic group, including those with no DR, had a significantly reduced PhNR amplitude (P < 0.05) when compared with controls. PhNR was found to reduce in amplitude with increasing severity of DR (P < 0.05), with more significance in B/Y. Receiver operating characteristic showed highest area under the curve in B/Y PhNR (94%, P < 0.001), with maximum sensitivity and specificity of 88% and 87%, respectively.

Conclusion:

Changes in the amplitude and implicit time of ERG can reflect the severity of DR. PhNR amplitudes, especially B/Y PhNR, appear to be significantly reduced even in eyes with no DR.

Comparison between broadband and monochromatic photopic negative response in full-field electroretinogram in controls and subjects with primary open-angle glaucoma

PURPOSE

A prospective, cross-sectional, case-control study was conducted to investigate the role of broadband and monochromatic photopic negative response (PhNR) of the full-field flash electroretinogram (ERG) in the evaluation of ganglion cell damage in primary open-angle glaucoma (POAG) subjects.

METHODS

Subjects with POAG and age-matched normal subjects were recruited from the outpatient department of a tertiary eye care center in South India. A total of 25 patients with POAG and 50 age-matched normal subjects were recruited. ERG was recorded using broadband (3.5 cd.s/m² white stimulus on 10 cd/m² white background) and monochromatic (3.5 cd.s/m² red stimulus on 10 cd/m² blue background and 1 cd.s/m² blue stimulus on 10 cd/m² yellow background) stimuli.

RESULTS

The reduction in PhNR amplitude in POAG compared to normal individuals was higher in red-on-blue PhNR [26.37 µV; p < 0.001, confidence interval (CI) 19.34 to 33.4] as compared to broadband stimuli (16.41 µV; p < 0.001, CI 8.68 to 24.13), and blue on yellow (21.96 µV; p < 0.001, CI 10.12 to 33.8). Red-on-blue PhNR amplitudes correlated better with mean deviation (MD; r = - 0.66, p < 0.05), pattern standard deviation (PSD; r = - 0.4, p = 0.04), visual field index (VFI; r = - 0.58, p < 0.05), and retinal nerve fiber layer thickness (r = - 0.67, p < 0.05) in comparison with broadband and monochromatic blue-on-yellow PhNR. Receiver operating characteristic curve revealed largest area under the curve (0.89) in red-on-blue PhNR compared to broadband (0.76) and blue on yellow (0.74). The sensitivity and specificity was also higher in red-on-blue PhNR (72% and 80%, respectively) as compared to the other stimuli (sensitivity and specificity of broadband 0.68 and 0.7, blue on yellow 0.64 and 0.7, respectively).

CONCLUSION

Correlation of PhNR with Humphrey visual field parameters and retinal nerve fiber layer thickness showed that red-on-blue PhNR can be a useful additional tool for clinical assessment of retinal ganglion cell dysfunction in glaucoma patients. Red-on-blue PhNR was more sensitive as compared to white-on-white and blue-on-yellow PhNR in identifying ganglion cell dysfunction and correlates well with other structural and functional tests for glaucoma such as MD, PSD, VFI, and RNFL thickness.

Reduced-fluence photodynamic therapy and anti-vascular endothelial growth factor for polypoidal choroidal vasculopathy in an Indian population

AIMS

The aim was to study the efficacy of combined therapy with reduced-fluence photodynamic therapy (RFPDT) and intravitreal bevacizumab/ranibizumab from the Indian subcontinent.

SETTINGS AND DESIGN

This was a single-center, retrospective interventional study.

METHODS

Thirty-five eyes of 34 patients diagnosed with polypoidal choroidal vasculopathy were included. All the patients underwent RFPDT, followed by intravitreal bevacizumab/ranibizumab.

STATISTICAL ANALYSIS USED

SPSS software, version 17.0 (SPSS Inc., Chicago, IL, USA) was used to compare the logarithm of the minimal angle of resolution visual acuity at presentation and final follow-up. P< 0.05 was considered statistically significant.

RESULTS

Regression of polyps after a single session of RFPDT was seen in five eyes; multiple sessions of treatment were required in thirty eyes. An average number of intravitreal anti-vascular endothelial growth factor (anti-VEGF) injections given were 4 ± 1.9 and average number of PDT sessions were 1.2 ± 0.5. Visual acuity improvement was seen in 21 (60%) eyes (P < 0.001), decrease in visual acuity was seen in 7 (20%) eyes (P = 0.016), and in 7 eyes (20%), vision remained stable. Regression of polypoidal lesions was seen in 80% of cases. No complications of massive subretinal hemorrhage or breakthrough vitreous hemorrhage were noted in our patients. The mean follow-up period was 18 months (range, 12-24 months).

CONCLUSIONS

RFPDT with anti-VEGF is safe and effective treatment with polyp regression and vision improvement in 80% of cases, without any complication of subretinal hemorrhage/vitreous hemorrhage.

Effect of axial length on full-field and multifocal electroretinograms

PURPOSE

The aim was to investigate the effect of axial length on full-field electroretinogram (ffERG) and multifocal electroretinogram (mfERG) in young Indian subjects.

METHODS

One hundred subjects (44 male) with refractive errors from +0.50 to -18.00 DS and no myopic retinopathy underwent axial length measurement. ffERG was measured, which included scotopic and photopic responses according to International Society for Clinical Electrophysiology of Vision (ISCEV) guidelines. The mfERG was recorded after correcting for refractive error according to ISCEV standards. The dark-adapted and light-adapted parameters of ffERG and N1, P1 parameters of six rings in mfERG were analysed with axial length, controlled for refractive error. The subjects were divided into seven groups based on axial length. The b/a ratio of dark-adapted and light-adapted 3.0 ffERG and P1/N1 ratio of mfERG amplitudes were analysed for seven groups of axial length.

RESULTS

The axial length ranged from 21.79 to 30.55 mm. Significant negative correlations were noted for ffERG and mfERG amplitudes, whereas implicit times showed minimal delay with increase in axial length. In ffERG, the scotopic responses were more decreased compared to photopic responses. In mfERG, P1 and N1 amplitudes were significantly decreased in all the rings in all groups and more reduction was noted in the central ring compared to peripheral rings. The P1 amplitudes were more affected as compared to N1 amplitudes. The light-adapted and dark-adapted 3.0 ERG b/a ratio and P1/N1 ratio for seven axial length groups did not show statistically significant difference. The ERG parameters were not significant with refractive error.

CONCLUSION

This study quantifies the relationship of axial length with ffERG and mfERG parameters in a young Indian population. Although the amplitudes were reduced significantly, the implicit times were not significantly affected. The ERG parameters were more related to axial length than refractive error. Hence, interpretation of ffERG and mfERG parameters needs careful consideration in subjects with increasing axial length.

Next-generation sequencing confirms the implication of SLC24A1 in autosomal-recessive congenital stationary night blindness

Congenital stationary night blindness (CSNB) is a clinically and genetically heterogeneous retinal disorder which represents rod photoreceptor dysfunction or signal transmission defect from photoreceptors to adjacent bipolar cells. Patients displaying photoreceptor dysfunction show a Riggs-electroretinogram (ERG) while patients with a signal transmission defect show a Schubert-Bornschein ERG. The latter group is subdivided into complete or incomplete (ic) CSNB. Only few CSNB cases with Riggs-ERG and only one family with a disease-causing variant in SLC24A1 have been reported. Whole-exome sequencing (WES) in a previously diagnosed icCSNB patient identified a homozygous nonsense variant in SLC24A1. Indeed, re-investigation of the clinical data corrected the diagnosis to Riggs-form of CSNB. Targeted next-generation sequencing (NGS) identified compound heterozygous deletions and a homozygous missense variant in SLC24A1 in two other patients, respectively. ERG abnormalities varied in these three cases but all patients had normal visual acuity, no myopia or nystagmus, unlike in Schubert-Bornschein-type of CSNB. This confirms that SLC24A1 defects lead to CSNB and outlines phenotype/genotype correlations in CSNB subtypes. In case of unclear clinical characteristics, NGS techniques are helpful to clarify the diagnosis.

Comparison between fullfield electroretinography obtained from handheld and tabletop devices in normal subjects

OBJECTIVE

To compare full-field electroretinography (ERG) parameters obtained from Ephios handheld and VERIS tabletop ERG devices in normal subjects for interchangeable usability and reliability.

DESIGN

Comparison study.

PARTICIPANTS

Comparison of full-field ERG between two devices for 57 normal subjects.

METHODS

ERG was recorded for 57 normal subjects using tabletop device (VERIS 5.2.2X; Electro-Diagnostic Imaging Inc, San Mateo, Calif.) and handheld ERG device (Ephios handheld portable ERG system; ephios ab; Teknikringen, Linkoping, Sweden). Bland-Altman plot was done to measure the agreement between the 2 devices. Intraclass correlation coefficient (ICC) was calculated for amplitudes, implicit times, and b/a ratio to assess the reliability. Coefficient of variation (CV = 100 × [standard deviation/mean]) with 95% CI was calculated to measure the variability between the devices. Wilcoxon sign rank test was used to assess the repeatability of the Ephios handheld device.

RESULTS

The mean a-wave and b-wave amplitudes of dark-adapted 3.0 ERG for the tabletop were 220.3 ± 52.6 and 471.5 ± 84.3 μV, respectively, whereas the mean a-wave and b-wave amplitudes in the same scotopic setting for the handheld device were 152.6 ± 34.2 and 379.7 ± 75.9 μV, respectively. The values represent mean ± standard deviation. The ICC of b/a ratio was 0.660 between the devices. The amplitudes CV of tabletop and handheld ERG devices ranged from 17.9% to 29.1% and from 22.4% to 30.1%, respectively.

CONCLUSIONS

The pattern of waveform of the Ephios handheld device is similar to the VERIS tabletop device. The ERG parameters showed variability between the 2 devices. Hence Ephios handheld ERG device can be used along with its normative data for measuring ERG. Because of variability, the devices cannot be used interchangeably.

Molecular profiling of complete congenital stationary night blindness: a pilot study on an Indian cohort

PURPOSE

Congenital stationary night blindness (CSNB) is a non-progressive retinal disorder that shows genetic and clinical heterogeneity. CSNB is inherited as an autosomal recessive, autosomal dominant, or X-linked recessive trait and shows a good genotype-phenotype correlation. Clinically, CSNB is classified as the Riggs type and the Schubert-Bornschein type. The latter form is further sub-classified into complete and incomplete forms based on specific waveforms on the electroretinogram (ERG). There are no molecular genetic data for CSNB in the Indian population. Therefore, we present for the first time molecular profiling of eight families with complete CSNB (cCSNB).

METHODS

The index patients and their other affected family members were comprehensively evaluated for the phenotype, including complete ophthalmic evaluation, ERG, fundus autofluorescence, optical coherence tomography, and color vision test. The known gene defects for cCSNB, LRIT3, TRPM1, GRM6, GPR179, and NYX, were screened by PCR direct sequencing. Bioinformatic analyses were performed using SIFT and PolyPhen for the identified missense mutations.

RESULTS

All eight affected index patients and affected family members were identified as having cCSNB based on their ERG waveforms. Mutations in the TRPM1 gene were identified in six index patients. The two remaining index patients each carried a GPR179 and GRM6 mutation. Seven of the patients revealed homozygous mutations, while one patient showed a compound heterozygous mutation. Six of the eight mutations identified are novel.

CONCLUSIONS

This is the first report on molecular profiling of candidate genes in CSNB in an Indian cohort. As shown for other cohorts, TRPM1 seems to be a major gene defect in patients with cCSNB in India.

A threshold mechanism mediates p53 cell fate decision between growth arrest and apoptosis

The p53 tumor suppressor responds to certain cellular stresses by inducing transcriptional programs that can lead to growth arrest or apoptosis. However, the molecular mechanisms responsible for choosing between these two cell fates are not well understood. Previous studies have suggested that p53 selectively activates proarrest target genes, due to the higher affinity of p53 for their promoters compared with proapoptotic genes. Here we show using microarray and chromatin immunoprecipitation that p53 binds to and transcriptionally activates both its proarrest and proapoptotic target genes proportionally to induced p53 expression levels. Further, we provide evidence that to trigger apoptosis, cells must overcome an apoptotic threshold, whose height is determined by expression levels of p53 and its targets, the duration of their expression and the cellular context. We demonstrate in multiple cells lines that below this threshold, expression levels of p53 and its targets were sufficient to induce arrest but not apoptosis. Above this threshold, p53 and its targets triggered extensive apoptosis. Moreover, lowering this threshold with inhibitors of antiapoptotic Bcl-2 family proteins sensitized cells to p53-induced apoptosis. These findings argue that agents that lower the apoptotic threshold should increase the efficacy of p53-mediated cancer therapy.

Real-time detection of cruciform extrusion by single-molecule DNA nanomanipulation

During cruciform extrusion, a DNA inverted repeat unwinds and forms a four-way junction in which two of the branches consist of hairpin structures obtained by self-pairing of the inverted repeats. Here, we use single-molecule DNA nanomanipulation to monitor in real-time cruciform extrusion and rewinding. This allows us to determine the size of the cruciform to nearly base pair accuracy and its kinetics with second-scale time resolution. We present data obtained with two different inverted repeats, one perfect and one imperfect, and extend single-molecule force spectroscopy to measure the torque dependence of cruciform extrusion and rewinding kinetics. Using mutational analysis and a simple two-state model, we find that in the transition state intermediate only the B-DNA located between the inverted repeats (and corresponding to the unpaired apical loop) is unwound, implying that initial stabilization of the four-way (or Holliday) junction is rate-limiting. We thus find that cruciform extrusion is kinetically regulated by features of the hairpin loop, while rewinding is kinetically regulated by features of the stem. These results provide mechanistic insight into cruciform extrusion and help understand the structural features that determine the relative stability of the cruciform and B-form states.

Analysis of large-scale sequencing of small RNAs

The advent of large-scale sequencing has opened up new areas of research, such as the study of Piwi-interacting small RNAs (piRNAs). piRNAs are longer than miRNAs, close to 30 nucleotides in length, involved in various functions, such as the suppression of transposons in germline. Since a large number of them (many tens of thousands) are generated from a wide range of positions in the genome, large-scale sequencing is the only way to study them. The key to understanding their genesis and biological roles is efficient analysis, which is complicated by the large volumes of sequence data. Taking account of the underlying biology is also important. We describe here novel analyses techniques and tools applied to small RNAs from germ cells in D. melanogaster, that allowed us to infer mechanism and biological function.

RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs

Use of RNA interference (RNAi) in forward genetic screens is proliferating. Currently, short-interfering RNAs (siRNAs) and short-hairpin RNAs (shRNAs) are being used to silence genes to tease out functional information. It is becoming easier to harness RNAi to silence specific genes, owing to the development of libraries of readymade shRNA and siRNA gene-silencing constructs by using a variety of sources. RNAi Codex, which consists of a database of shRNA related information and an associated website, has been developed as a portal for publicly available shRNA resources and is accessible at . RNAi Codex currently holds data from the Hannon–Elledge shRNA library and allows the use of biologist-friendly gene names to access information on shRNA constructs that can silence the gene of interest. It is designed to hold user-contributed annotations and publications for each construct, as and when such data become available. We will describe features of RNAi Codex and explain the use of the tool.

Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots

Recent studies of human populations suggest that the genome consists of chromosome segments that are ancestrally conserved ('haplotype blocks'; refs. 1-3) and have discrete boundaries defined by recombination hot spots. Using publicly available genetic markers, we have constructed a first-generation haplotype map of chromosome 19. As expected for this marker density, approximately one-third of the chromosome is encompassed within haplotype blocks. Evolutionary modeling of the data indicates that recombination hot spots are not required to explain most of the observed blocks, providing that marker ascertainment and the observed marker spacing are considered. In contrast, several long blocks are inconsistent with our evolutionary models, and different mechanisms could explain their origins.

Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order

We have investigated possible collinearity between the genomes of rice and Arabidopsis by comparing 126 annotated and mapped rice BAC sequences (approximately 20 Mb of sequence) with the annotated and complete Arabidopsis genome (approximately 115 Mb). Although we were able to identify several regions in which gene order is preserved, they are relatively small, and are interrupted by noncollinear genes. Computer simulation showed that these microscale collinearities are above the expectation for a random process. On the other hand, the order of exons within homologous genes (<2.5 kb) was preserved, as expected.

A high-resolution radiation hybrid map of the human genome draft sequence

We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.